Ran Xu,Chuanqing Sun*

State Key Laboratory of Plant Physiology and Biochemistry,China Agricultural University,Beijing 100193,China

Keywords:Oryza genus Wild rice Cultivated rice Domestication

ABSTRACT Domestication of crops is one of the greatest inventions of the human race and has played a vital role in the progress of human civilization.Understanding the genetic mechanisms of crop domestication could shed light on its history and would advance crop breeding.Cultivated rice species,which were domesticated from wild rice species,are important food crops worldwide.Morphological traits,physiological characteristics,and ecological adaptability of cultivated rice are very different from those characters of wild rice.In this review,we summarize current knowledge of the genetic mechanisms underlying these differences between wild and cultivated rice and discuss the application of wild rice species in modern breeding.

1.Introduction

The domestication of crops was critical for the emergence of agricultural societies and the development of human civilization.Rice is one of the earliest-domesticated crops,as well as a model species for cereal crops.Investigating the genetic mechanisms of rice domestication is beneficial for revealing the history of rice domestication,understanding genetic mechanisms controlling important traits,mining favorable alleles from wild rice,and developing improved rice cultivars.

Rice belongs to the Oryza genus,which is composed of more than 20 species[1-3].By cytogenetic analysis,Oryza species can be classified into 11 genome types,six of which are diploid(AA,BB,CC,EE,FF,and GG),and the others tetraploid(BBCC,CCDD,HHJJ,HHKK,and KKLL).The two cultivated rice species,Asian(O.sativa L.)and African(O.glaberrima),are AA-genome species.

Asian cultivated rice,which was domesticated from the wild O.rufipogon species,is widely planted worldwide.Asian cultivated rice is composed of two major subspecies,O.sativa ssp.geng/japonica and xian/indica[4,5].Although archaeological evidence shows that the domestication of Asian rice began as early as 9000 years ago in the Yangtze Valley of China[6-8],the origin of Asian cultivated rice is still a relatively complex and contentious topic[9,10].Studies[11-13]suggested that Asian cultivated rice cultivars have a single origin with multiple introgressions.It was speculated that the geng landraces were de novo domesticated in southern China and then spread to other parts of Asia.Subsequently,the xian landraces arose from crosses between the domesticated geng rice and local wild or semi-wild rice.However,recent studies[4,14]support multiple independent domestications of Asian rice.They indicate that the geng landraces originated in China,whereas the xian landraces were domesticated independently from local wild rice accessions in China and India.

Compared with Asian cultivated rice,African rice is planted in a limited area.Moreover,it is gradually being replaced in Africa by Asian rice owing to its lower yield[15,16].Independently of the domestication of Asian cultivated rice,African cultivated rice was domesticated from its wild progenitor O.barthii about 3000 years ago[17-20].Although it has been proposed[20,21]that African rice domestication occurred in the Inner Niger Delta,recent studies[22,23]have suggested that it was multiregional.Thus,the origin of African rice is still debated.

During the domestication from wild rice species to cultivated rice species,a series of marked changes in morphological traits(Fig.1),physiological characteristics,and ecological adaptability have occurred.These changes include transition from prostrate to erect growth,loss of grain shattering,shortened awns or awnlessness,changed hull and grain color,reduced grain dormancy,changed panicle architecture,increased grain number and weight,and improved regional adaptability.All of these changes have contributed to the improvement of agronomic traits that were favored by our human ancestors.Transition from prostrate to erect growth,loss of grain shattering,shortened awns or awnlessless,and transition from loose to compact panicles are essential for cultivationand harvest and thus were key transitions in the earliest steps of rice domestication.Grain color,grain size,grain number,grain dormancy,and ecological adaptability were changed to meet human needs during the post-domestication(improvement)process.With the development of molecular biology and genomics,increasing numbers of genes controlling these changes have been identified,greatly advancing our knowledge of the genetic mechanisms underlying rice domestication and improvement.

Fig.1.Differences in morphological traits of wild and cultivated rice.(A,B)Plants of wild rice(O.rufipogon)(A)and Asian cultivated rice(B).(C,D)Panicles of O.rufipogon(C)and Asian cultivated rice(D).(E,F)Grains of O.rufipogon(E)and Asian cultivated rice(F).Scale bars,5 mm.(G,H)Hulled grains of O.rufipogon(G)and Asian cultivated rice(H).Scale bars,5 mm.

Several excellent reviews [6,16,19,24-27]have provided detailed summaries of and useful information about the genomics of Oryza species and the history of rice domestication.Here we focus on genetic mechanisms underlying the changes of morphological traits,physiological characteristics,and ecological adaptability during rice domestication and improvement,and discuss the potential application of wild rice species in breeding modern rice cultivars.

2.Transition from prostrate to erect growth and improvement of plant architecture

The transition from prostrate to erect growth is one of the most typical features of rice domestication.In wild conditions,the prostrate growth habit of wild rice species may contribute to its survival and propagation.In artificial conditions,the erect growth habit of cultivated rice species is beneficial for increasing planting density and yield.Several genes that contributed to the transition from prostrate to erect growth during rice domestication have been identified.

PROG1(PROSTRATE GROWTH 1),which encodes a zinc-finger transcription factor,is a well-known gene[28-30]that controls the transition from prostrate to erect growth that occurred during Asian rice domestication.The wild PROG1 allele results in a large tiller angle.The mutated prog1 allele,which is considered a nonfunctional allele in tiller angle regulation,results in a small tiller angle.All tested Asian cultivated rice accessions harbor the prog1 allele,whereas some Asian wild rices harbor the PROG1 and others the prog1 allele[29].Thus,prog1 is a single-origin allele and was selected during Asian rice domestication.The mutated prog1 also results in large panicles with more grains and thereby increased grain yields[29].Thus,selection of the prog1 allele contributed to not only erect growth but also higher yield of Asian cultivated rice.

A recent study[31]showed that a 110-kb deletion closely linked to PROG1 also contributed to the transition from prostrate to erect growth in Asian cultivated rice.This deletion harbors a tandem repeat of seven zinc-finger genes,which are homologs of PORG1.This multiple zinc-finger gene-containing tract,including PROG1,is referred to as RPAD(RICE PLANT ARCHITECTURE DOMESTICATION)[31].Like PROG1,this 110-kb deletion represents a single evolutionary event,as all tested Asian cultivated rices carry it[31].However,in contrast to PROG1,it is not found in all tested Asian wild rices.It was accordingly speculated that it occurred during Asian rice domestication,whereas the prog1 allele originated earlier and independently.

A similar 113-kb deletion at the RPAD locus occurred in African cultivated rice[31].However,in Asian cultivated rice the first zincfinger gene(prog1)at the RPAD locus was retained,while in Africancultivated rice the last zinc-finger gene was retained.Thus,this 113-kb deletion in African cultivated rice originated independently from the 110-kb deletion in Asian cultivated rice,revealing a parallel selection process in the RPAD locus during domestication.Supporting this idea,a large-scale genomic analysis[32]of African rice revealed that the entire PROG1 gene was deleted in assembled genomes of African cultivated rice.The 113-kb deletion occurred in all tested African wild rices,revealing it too as a single-origin event.

PROG7(PROSTRATE GROWTH 7),a zinc-finger gene on chromosome 7,has been shown[33]to play a critical role in the prostrate growth of African wild rice.PROG7 corresponds to the retained zinc-finger allele(prog7)at the RPAD locus in African cultivated rice[31].In contrast to prog1,prog7 encodes a protein that functions in regulating tiller angle,as transgenic plants overexpressing prog7 form a large tiller angle[33].Variations in the promoter of prog7 result in reduced gene expression in the tiller base and thus the reduced tiller angle of African cultivated rice.All tested African cultivated rice accessions harbor the prog7 allele,suggesting that it too is a single-origin allele and was selected and fixed during African rice domestication.

TAC1(Tiller Angle Control 1)is the first cloned gene underlying a major quantitative trait locus(QTL)for tiller angle in rice[34].TAC1 encodes a 259-amino-acid protein with unknown function.The wild TAC1 allele results in large tiller angle.The mutated tac1 allele,which harbors an A-to-G mutation in the 3′-splicing site of the fourth intron,confers small tiller angle and compact plant architecture.The A-to-G mutation of the tac1 allele causes abnormal intron splicing and results in shortened and unstable mRNA,although the protein sequence encoded by the tac1 allele is identical to that encoded by TAC1.All tested geng accessions harbor the mutated tac1 allele,whereas most xian accessions and all tested Asian wild rice accessions carry the wild TAC1 allele[34-36].Thus,selection of the tac1 allele has contributed to the compact plant architecture of Asian geng rice.

A recent study[37]showed that the presence of the tac1 allele contributes to the yield advantages of hybrid rice.Compared with the homozygous TAC1/TAC1 genotype,the heterozygous TAC1/tac1 genotype does not affect grain yield per plant and allows an increase in planting density that increases grain yield per unit area.In most three-line hybrid rice cultivars,the female parents carry the tac1 and the male parents the TAC1 allele.However,only a few two-line hybrid rice cultivars carry the tac1 allele,suggesting that it might be possible to increase grain yield of two-line cultivars by employing this allele.

Besides TAC1,a genome-wide association study[35]showed that TAC3(Tiller Angle Control 3)and D2(Dwarf 2)also determine tiller angle in Asian rice cultivars.TAC3 encodes a conserved hypothetical protein,and overexpression of TAC3 results in large tiller angle.D2 is involved in the biosynthesis of brassinosteroid[38],and loss of function of D2 leads to small tiller angle.Although haplotype analysis suggested that TAC3 and D2 also have been subjected to selection during geng domestication,the functional variants of TAC3 and D2 in rice cultivars have yet to be identified.

TIG1(TILLER INCLINED GROWTH 1)is another key gene contributing to compact plant architecture of Asian rice[39].TIG1 encodes a class-II TCP transcription factor and may regulate tiller growth by promoting the expression of several genes influencing cell expansion:EXPA3,EXPB5,and SAUR39.Variations in the promoter of TIG1 reduce the expression of TIG1 on the adaxial side of the tiller base and lead to small tiller angle.Most xian accessions carry the mutated tig1 allele(with lower expression),whereas most tested geng rice and wild rice accessions carry the wild TIG1 allele(with higher expression).Thus,the tig1 allele was selected during the improvement of xian rice.Genetic analyses showed that TIG1 acts additively with PROG1 and TAC1,suggesting that TIG1,PROG1,and TAC1 regulate tiller angle via different molecular pathways.

In summary,RPAD,TAC1,and TIG1 are three key loci involved in the transition from prostrate to erect growth and the improvement of rice plant architecture(Fig.2C).Parallel selection of the RPAD locus operated in the transitions from prostrate to erect growth in both Asian and African rice(Fig.2A,B).Selection of the RPAD and TAC1 loci contributed to the erect growth and compact plant architecture of Asian geng rice,and selection of the RPAD and TIG1 loci resulted in the erect growth of Asian xian rice(Fig.2C).Only one zinc-finger gene was coincidentally maintained in the RPAD locus of both Asian and African cultivated rice(Fig.2A,B),although the deletion events were independent.The retained prog1 and prog7 in cultivated rice are respectively nonfunctional and weak alleles with respect to their effect on tiller angle regulation(Fig.2A,B).Thus,it is still unclear whether the retention of a nonfunctional or weak zinc-finger allele in both Asian and African cultivated rice is a mere coincidence or a result of intricate selection and whether the prog1 and prog7 alleles of cultivated rice have other basic developmental or defense functions besides tiller angle regulation.Knockout of prog1 and prog7 in cultivated rice accessions using the CRISPR/Cas9 method would shed light on these questions.The molecular mechanisms by which these zinc-finger genes in the RPAD locus regulate tiller growth await investigation.

3.Loss of grain-shattering habit

Loss of grain-shattering habit is another key step of rice domestication.For wild rice,natural grain shattering after maturity is beneficial for guaranteeing propagation.However,grain shattering is inconvenient for harvesting.Loss of the grain-shattering habit in cultivated rice expedites its harvest and reduces yield loss.The abscission layer between sterile lemma and pedicel,which consists of small thin-walled cells,plays a critical role in seed shattering[40].Wild rice species have a complete abscission layer and the cell wall of the thin-walled cells is degraded after maturity,leading to seed shattering.In cultivated rice,the abscission layer is incomplete or abnormal,reducing shattering.Several genes contributing to the loss of grain-shattering habit during rice domestication have been identified in recent years.

SH4(Shattering 4)/SHA1 corresponds to a major QTL for grainshattering habit in Asian rice[40-42].SH4/SHA1 encodes a protein containing an N-terminal MYB-type DNA-binding domain and a C-terminal nuclear localization signal.Mutation of the 79th amino acid(lysine to asparagine)in the MYB-type domain of SH4/SHA1 was responsible for reduction of grain shattering during the domestication of Asian rice.The non-shattering sh4 is a singleorigin allele and was fixed in all tested Asian cultivated rices[40,42,43],suggesting that the sh4 allele originated in the early stages of Asian rice domestication.Although the domestications of Asian and African rice were independent,the ortholog of SH4/SHA1 in African rice,GL4(GRAIN LENGTH 4),also contributed to the change in grain-shattering ability during African rice domestication,revealing a parallel domestication process at the SH4/SHA1/GL4 locus[44,45].A single-nucleotide-polymorphism nonsense mutation in the GL4 locus of some African cultivated rice accessions results in a truncation of the C-terminal sequence and abolishes the nuclear localization of GL4,reducing grain shattering.Hereafter,this non-shattering allele of GL4 in African rice is referred as gl4.With respect to reduction of grain shattering,the non-shattering gl4 allele is a strong and sh4 a weak allele.However,interestingly,gl4 in African cultivated rice also results in small grains,whereas the weak sh4 allele does not affect grain size[45](Fig.3A).Thus,although gl4 contributes to loss of grain shattering,it also results in yield reduction.Selection of the non-shattering gl4during the domestication process of African rice was imperfect,and the replacement of gl4 by sh4 could increase grain size and thus improve the yield of African rice.Another interesting phenomenon at the SH4/SHA1/GL4 locus is that the heterozygous sh4/gl4 results in a shattering phenotype[44,46](Fig.3A).This heterozygous-induced throwback phenomenon could be caused by functional complementation of the sh4 and gl4 alleles.However,its molecular mechanism awaits elucidation.

Fig.2.Genetic basis of the transition from prostrate to erect growth during rice domestication.(A,B)Parallel selection of the RPAD locus in Asian and African rice.The RPAD locus consists of multiple zinc-finger genes.Green boxes represent zinc-finger genes that function in increasing tiller angle.The light green box represents a weak allele.Gray boxes correspond to nonfunctional zinc-finger genes.Blue boxes represent zinc-finger genes of undetermined function.During the domestication process,110-kb and 113-kb deletions occurred in the respective RPAD loci of Asian and Africa rice,and only one zinc-finger gene was coincidentally retained in both Asian and African cultivated rice.The retained prog1 in Asian cultivated rice is considered a nonfunctional allele in tiller angle regulation and the retained prog7 in African cultivated rice is a weak allele increasing tiller angle.(C)Selections of the prog1 allele in the RPAD locus,the 110-kb deletion in the RPAD locus,and the tac1 allele contributed to the erect growth and improved plant architecture of Asian geng/japonica rice.Selections of the prog1 allele in the RPAD locus,the 110-kb deletion in the RPAD locus,and the tig1 allele contributed to the erect growth and improved plant architecture of Asian xian/indica rice.

OsSH1(Oryza sativa Shattering 1),which encodes a YABBY transcription factor,is another gene controlling grain shattering[47,48].OsSH1 and its orthologs in maize and sorghum have undergone parallel selection during the domestication of these three cereal crops [47].OsSH1 corresponds to a minor-effect QTL contributing to the differences in grain shattering ability between Asian wild and cultivated rice species[49-51].However,although an artificial mutant of OsSH1 exhibited a non-shattering phenotype[47],the natural causal variant of OsSH1 explaining the difference in grain-shattering ability between Asian wild and cultivated rice has not yet been identified.ObSH3(Oryza barthii Shattering 3),which is allelic to OsSH1,contributed to the loss of grainshattering ability during the domestication of African rice[17,22,32,48].A 45.5-kb deletion containing the entire ORF of ObSH3,hereafter referred as the sh3 allele,results in an abnormal abscission layer and a decrease of grain shattering in African cultivated rice populations.Thus,the OsSH1/ObSH3 locus too has undergone parallel selection during the domestication of Asian and African rice,although OsSH1 corresponds to a minor-effect QTL.Genetic analysis showed that the OsSH1/ObSH3 and SH4/SHA1/GL4 loci act additively to control grain shattering ability,and African cultivated varieties harboring both the non-shattering gl4 and sh3 alleles exhibit complete non-shattering phenotypes.All tested African cultivated rice accessions harbor both or one of the nonshattering gl4 and sh3 alleles,suggesting that OsSH1/ObSH3 and SH4/SHA1/GL4 are two key contributors to the loss of grain shattering in African cultivated rice.

qSH1(QTL for seed shattering on chromosome 1)is another major QTL controlling grain shattering in Asian rice and explains a large part of the shattering difference between xian and geng accessions[52].The qSH1 gene encodes a BEL1-like homeobox protein.A single-nucleotide substitution in the 5′regulatory region of theqSH1 gene reduces its expression and results in an abnormal abscission layer,ultimately reducing grain-shattering ability.The non-shattering allele of qSH1 was found only in temperate geng accessions and not in other groups of Asian cultivated rice,suggesting that qSH1 was a selection target during the domestication of temperate geng cultivars[43,52].Another shattering gene,SH5,also encodes a member of the BEL1-like homeobox protein family[53].Overexpression of SH5 reduces grain shattering,whereas its knockdown increases shattering.Although there is no evidence for selection of SH5 in Asian cultivated rice,genomic analysis showed that SH5 is located in a region under selection during the domestication of African rice and an in-frame deletion in SH5 was fixed in African rice,suggesting that selection of SH5 contributed to the non-shattering phenotype of African rice[32].A KNOX protein,OSH15,could interact with SH5 to regulate grain shattering ability by directly repressing the expression of a lignin biosynthesis gene[54].

Fig.3.Genetic mechanisms underlying the loss of seed shattering during rice domestication.(A)Parallel selections of the SH4/SHA1/GL4 gene in Asian and African rice.The structures of proteins encoded by the different alleles of S H4/SHA1/GL4 are shown.Blue boxes represent the MYB-type DNA-binding domain and orange lines indicate the C-terminal nuclear localization signal.The protein encoded by the sh4 allele has an amino acid change(K89N).The gl4 allele encodes a truncated protein.Compared with sh4,gl4 is a strong allele,which not only leads to a non-shattering phenotype but also results in small grains.Most wild rices harbor the wild SH4/SHA1/GL4.All Asian cultivated rice accessions harbor the weak non-shattering sh4 allele.More than 80%of tested African cultivated rice accessions carry the strong non-shattering gl4.Plants with heterozygous sh4/gl4 exhibit a‘‘throwback”shattering phenotype,implying that the sh4 and gl4 alleles are functionally complementary in ensuring the normal development of abscission layer.(B)Genetic mechanisms of grain shattering.Several grain-shattering genes have been identified,some of which have undergone selection during rice domestication.SH4/SHA1/GL4 and OsSH1/ObSH3(labeled in orange)have undergone selection during the domestication of both Asian and African rice.The non-shattering allele of qSH1(labeled in green)was selected during the domestication of Asian geng/japonica rice,whereas selection of SH5(labeled in blue)may contribute to the reduced grain shattering of African rice.Although the detailed molecular mechanisms of grain shattering are still largely unknown,several genes act together to regulate grain shattering,including SH4/SHA1/GL4,qSH1,SH5,OSH15,SHAT1,and SNB1.SH4/SHA1/GL4 could promote SHAT1 expression.SHAT1 and SH4/SHA1/GL4 act genetically upstream of qSH1 to maintain the expression of SHAT1 and SH4/SHA1/GL4 in the abscission layer.SH5 promotes the expression of SHAT1 and SH4/SHA1/GL4.SNB binds to the promoter of qSH1 and SH5 to promote their expression.OSH15 interacts with SH5 to regulate grain shattering.Arrowed lines and T-shaped line represent respectively‘‘promote”and‘‘inhibit”.

SHAT1(SHATTERING ABORTION1),which encodes an APETALA2 transcription factor,influences the development of the abscission layer[55].Genetic analysis showed that SH4/SHA1/GL4,which functions in the early abscission-layer development,promoted SHAT1 expression in the abscission layer.SHAT1 and SH4/SHA1/GL4 act genetically upstream of qSH1 to maintain the expression of SHAT1 and SH4/SHA1/GL4 in the abscission layer,suggesting the operation of a positive feedback loop among these genes.SH5,mentioned above,also promoted the expression of SHAT1 and SH4/SHA1/GL4[53].SNB1(SUPERNUMERARY BRACT),which encodes another APETALA2 transcription factor and functions in the transition from spikelet meristem to floral meristem,is also involved in regulating grain shattering and grain size[56-59].A genome-wide association analysis[60]showed that natural variation in SNB contributed to differences in grain size in natural populations.It would be interesting to know whether natural variation in SNB contributes to differences in grain-shattering ability among natural populations.SNB bound to the promoter of qSH1 and SH5 to promote their expression[56].

Other genes involved in abscission-layer development are OsCPL1(Oryza sativa CTD phosphatase-like 1)and OsGRF4(Oryza sativa Growth-Regulating Factor 4)[61,62].Loss of function of OsCPL1 increases grain shattering,whereas elevated expression of OsGRF4 reduces grain shattering.The interactions of OsCPL1 and OsGRF4 with the genes described above are still unclear.

In summary,several critical grain-shattering genes have been identified,some of which have undergone selection during rice domestication(Fig.3B).The non-shattering alleles of SH4/SHA1/GL4 and OsSH1/ObSH3 were selected during the domestications of both Asian and African rice.The non-shattering allele of qSH1 was selected during the domestication of Asian geng rice.Selection of SH5 may have contributed to the reduced grain shattering of African rice.

4.Change of panicle architecture and increase of grain yield

Panicle architecture is another major target of rice domestication and improvement.Compared with the loose panicles with fewer and smaller grains of wild rice,panicles of cultivated rice accessions are generally compact and bear more and larger grains.Many genes have been shown to function in regulating panicle shape,grain number,and grain weight in Asian rice[63-66],some of which have been subjected to selection during domestication and improvement.However,genes contributing to the improved panicle architecture of African cultivated rice are still largely unknown.

OsLG1(OsLIGULELESS1),which encodes a SBP(SQUAMOSA promoter Binding Protein)-domain transcription factor,functions in controlling the development of the ligule and auricle[67].Interestingly,OsLG1 is also a critical gene controlling the transition from loose to compact panicles during the domestication of Asian rice[68,69].A SNP located in the regulatory region of OsLG1 reduces its expression in the panicle pulvinus and leads to the compact panicle of Asian cultivated rice.

Grain number per panicle of cultivated rice is greater than that of wild rice.Several genes contributing to increased grain number in Asian cultivated rice have been identified.NOG1(NUMBER OF GRAINS 1)encodes an enoyl-CoA hydratase/isomerase[70].A 12-bp insertion in the promoter region of NOG1 increases its expression,and leads to increased grain number.FZP(FRIZZY PANICLE),which encodes an AP2/ERF domain transcription factor,functions in establishing floral meristem identity[71,72].Natural variations in the regulatory region of FZP reduce its expression and result in increased grain number[73-75].The FZP protein was targeted and degraded by the trypsin-like serine and cysteine protease NAL1(NARROW LEAF 1)[73,76].Natural variations in NAL1 also affect grain number,and a beneficial allele of NAL1 from a tropical geng rice accession increased the yield of xian accessions[77].Thus,natural variations in the NAL1-FZP module influence grain number.OsCKX2,which encodes a cytokinin oxidase/dehydrogenase,corresponded to a major QTL for grain number[78].Natural variations in OsCKX2 reduce its expression or abolish its function,consequently increasing the cytokinin level and leading to more grains.APO1(ABERRANT PANICLE ORGANIZATION1),which acts in the transition from rachis branch meristem to spikelet meristem[79-81],corresponded to a QTL for culm strength and grain number[82].APO1 encodes an F-box type E3 ligase.The beneficial allele of APO1 increases its expression and consequently enlarges the inflorescence meristem and results in more grains.Thus,natural variation in NOG1,FZP,NAL1,and APO1 contribute to increased grain number in cultivated rice.

Grains of cultivated rice accessions are generally larger and heavier than those of wild rice species.The molecular mechanisms underlying rice grain size and weight development have been studied[63,65,83].Several genes underlying QTL for grain size and weight have been cloned,including GW2[84],GS2/GL2[85-87],TGW2[88],OsLG3[89],qLGY3/OsLG3b[90,91],GS3[92],qGL3/GL3.1[93,94],GL3.3/TGW3[95-97],GS5[98],GW5/GSE5[99,100],TGW6[101],GW6a[102],GLW7[103],GL7/GW7/SLG7[104-106],and GW8[107].Beneficial alleles of some of these genes(TGW2,OsLG3,qLGY3/OsLG3b,GS3,GS5,GW5/GSE5,GLW7,GL7/GW7/SLG7,GW8)have been widely deployed in modern rice cultivars and have contributed to their large grains.

5.Shortened awns or awnlessness

Awn traits are important domestication traits.Seeds of wild rice species form long and barbed awns,whereas seeds of most cultivated rices produce very short or no awns.For seeds of wild rice,long and barbed awns are beneficial for dispersal on animal fur and wind,for avoiding being eaten by animals,and for selfseeding[108,109].However,for cultivated rice,awns impede harvesting,storing,and processing.Several key genes contributing to loss of awn during the domestication process of Asian rice have been identified,whereas genes causing the awnless phenotype in African cultivated rice have not.

An-1(Awn-1),which encodes a basic helix-loop-helix transcription factor,corresponds to a major QTL for awn length[110].An-1 is highly expressed in the apex of the lemma primordia and the subsequent awn primordia,and promotes continuous cell division,resulting a in long awn.Wild rice species harboring the wild An-1 allele form long awns.A transposon insertion in the promoter region or a 1-bp deletion in the coding sequence of An-1 is associated with the awnless phenotype in Asian cultivated rice.In comparison with wild species,the nucleotide diversity of An-1 is reduced in Asian cultivated rice accessions,implying that the An-1 locus has undergone strong artificial selection.An-1 is also involved in regulation of grain size and number.Mutated alleles of An-1 in cultivated rice lead to shorter but more grains and correspondingly increased grain yield.Thus,selection of mutated alleles of An-1 during the domestication of Asian rice led to both shortened awns and higher grain yield.

LABA1(LONG AND BARBED AWN1)/An-2(Awn-2)is another domestication gene,associated with the long and barbed awns in wild rice[111,112].A 1-bp deletion in the coding sequence of LABA1/An-2 in Asian cultivated rice abolishes the function of LABA1/An-2,disrupting awn elongation and awn barb formation.LABA1/An-2 encodes a homolog of LOG(Lonely Guy),which is a cytokinin-activating enzyme and is involved in the final step of cytokinin biosynthesis,suggesting that cytokinin functions in the formation of long and barbed awns in wild rice.Expression pattern analysis[111,112]showed that An-1 and LABA1/An-2 are expressed in respectively the earlier and later stages of awn primordium development,implying that An-1 is involved in awn initiation and LABA1/An-2 promotes awn elongation.Nucleotide diversity analysis[111,112]suggested that LABA1/An-2 has also undergone strong artificial selection during the domestication of Asian rice.Besides its role in awn elongation,An-2 also regulates grain number and tiller number.Selection of the mutated allele of An-2 during the domestication of Asian rice not only shortened awns but increased grain yields by increasing grain number per panicle and tiller number per plant[111,112].

GAD1(GRAIN NUMBER,GRAIN LENGTH AND AWN DEVELOPMENT1)/REF2(REGULATOR OF AWN ELONGATION 2)/GLA(Grain Length and Awn Development),which encodes a small signal peptide belonging to EPFL(EPIDERMAL PATTERNING FACTOR-LIKE)family,also functions in the formation of long awn in wild rice[113-115].The EPFL family peptides require posttranslational cleavage to produce mature peptides[116].SLP1(Subtilisin-like protease 1),which is expressed specifically in the young inflorescence,cleaves the precursor of GAD1/REF2/GLA to produce mature peptide,and the mature GAD1/REF2/GLA peptide promotes the elongation of awns and grains[115].EPFL-family peptides share a conserved region of six cysteine residues[117].A frameshift deletion in a GC-rich region of the GAD1/REF2/GLA CDS in Asian cultivated rice accessions destroys the C-terminal protein sequence,leads to the absence of two of six conserved cysteine residues,and causes shortened awns[113-115].GAD1/REF2/GLA is also involved in grain size and number regulation.Interestingly,haplotype and transgenic analyses showed[113]that the frameshift deletion in the coding region of GLA does not affect grain size,while a deletion in the promoter region of GLA results in short grains and does not affect awn development.The deletion in the promoter region also reduces the expression of GLA.Thus,it can be deduced that the mutated GAD1/REF2/GLA peptide withdestroyed C-terminal sequence is still functional in regulating grain length but not awn development,while the full-length GAD1/REF2/GLA peptide regulates both grain length and awn development(Fig.4).Why the mutated GAD1/REF2/GLA peptide is still functional in regulating grain size and how the full-length and mutated GAD1/REF2/GLA peptides functions differently in regulating awn and grain development await further study.

Fig.4.GAD1/REF2/GLA regulates the length of both awns and grains.GAD1/REF2/GLA encodes a EPFL-family short peptide,the precursor of which is composed of a signal peptide,a pro-peptide,and the C-terminal peptide that corresponds to the mature peptide.SLP1 cleaves the precursor of GAD1/REF2/GLA to produce mature peptide,which comprises six conserved cysteine residues(labeled with blue lines).Various alleles of GAD1/REF2/GLA were selected during the domestication process of Asian rice.The wildtype GLA allele in wild rice leads to long awns and long grains.The glaawn allele,which harbors a frame-shift deletion(labeled with a yellow triangle)in the coding sequence of GAD1/REF2/GLA,destroys the C-terminal protein sequence,leads to the absence of two of six conserved cysteine residues,and causes shortened awns.The glaawn/grain allele,which harbors not only the frameshift deletion in coding region but a deletion in the promoter region(labeled with a blue triangle),results in short awns and short grains.Thus,the mutated GAD1/REF2/GLA peptide with destroyed C-terminal sequence encoding by glaawn is still functional in regulating grain length.

Two other genes,DL(DROOPING LEAF)and OsETT2(Oryza sativa ETTIN2)also promote awn development in rice[118],although it is still unclear whether these two genes are involved in domestication.It has been shown[119]that loss of awns in African rice is caused by different genes,and a major QTL controlling awn length of African rice has been mapped to chromosome 6.Identification of genes contributing to awn shortening during the domestication of African rice would shed new light on the difference between the processes of domestication of Asian and African rice.

6.Changed grain color

Colors of the grain hull and pericarp are different in wild and cultivated rice(Fig.5).Wild rice species typically produce grains with black hull,while the hull of cultivated accessions is generally straw-white(golden colored or yellowish)[120].The pericarp of wild rice grains is red,whereas most of the Asian cultivated accessions produce white pericarps.In contrast to Asian cultivated rice,only a small fraction of African cultivated rice accessions produce grains with white pericarp;most produce grains with red pericarp.

The Bh4(Black hull 4)and Rc genes have been identified as contributing to the differences in grain hull and pericarp colors of wild and cultivated rice[120,121].Most tested Asian cultivated rice accessions harbor mutations in the coding region of Bh4,that disrupt the function of Bh4 and result in straw-white hulls[120].However,several accessions harboring the wild-type Bh4 allele also form straw-white hulls,suggesting that other genes may also contribute to the change of hull color in Asian cultivated rice.Supporting this idea,transgenic analysis showed that the wild-type Bh4 allele rescued the black-hull phenotype in xian accessions but not in geng accessions.Various other deletions in the coding region of Bh4 in African cultivated rice accessions are also associated with straw-white hull phenotypes[122],showing that Bh4 has undergone parallel selection in African and Asian rice.Rc encodes a basic helix-loop-helix(bHLH)protein that is involvedin proanthocyanidin synthesis[121,123].Most Asian cultivated rice accessions harbor a 14-bp deletion in the sixth exon of Rc,which leads to white pericarp.A small proportion of Asian cultivated rice accessions harboring a premature-stop allele of Rc produce grains with light red pericarp.Coincidentally,two of the three tested African cultivated rice accessions with white pericarp grains harbor a different premature-stop allele of Rc[124],suggesting that Rc also contributes to the change in pericarp color in African rice.

Fig.5.Genetic mechanisms underlying different grain color in wild and cultivated rice.A diagram showing the transition of grain color in Asian rice.Selection of the mutated alleles of Bh4 contributed to the transition from black hull to straw-white hull,and selection of the mutated alleles of Rc contributed to the transition of red pericarp to white pericarp.The use of pericarp-specific Kala4 contributed to the breeding of‘‘purple rice”cultivars.Use of the hull-specific S1 contributed to the breeding of‘‘purple hull”cultivars,and the hull-specific S1 must act together with C1 and A1 to ensure the hull-specific accumulation of purple color.

Although most of the Asian cultivated rice accessions produce grains with white pericarp,a very small proportion,referred to as‘‘purple rice”accessions,produce grains with dark purple pericarp.In these‘‘purple rice”accessions,an ectopically expressed Kala4 allele,which is highly expressed in the pericarp,contributes to the dark purple pericarp(purple grain)trait[125].Like Rc,Kala4 encodes a bHLH transcription factor and is involved in regulating anthocyanin biosynthesis.Besides‘‘purple rice”accessions,some,referred to as‘‘purple hull”accessions,produce grain with dark purple hulls.A three-gene system,C1-S1-A1,has been shown to regulate the dark purple-hull phenotype[126].C1 and a hullspecifically expressed S1 allele act in producing hull color,while A1 promotes the transition from brown to dark purple hull.S1 is allelic to Kala4,although how the variations lead to the hullspecific expression of S1 is unknown.The genetic mechanism underlying the different expression patterns of the hull-specific S1 and pericarp-specific Kala4 awaits elucidation.Wild and cultivated rices also show different anthocyanin accumulations in leaves,leading to different leaf color.Artificial selection of the C1 gene mentioned above and another gene,OsRb,contributed to the difference in anthocyanin accumulation between wild and cultivated rice[127].

Selection of mutated alleles of Bh4 and Rc thus contributed to the respective transitions of grains from black hull and red pericarp to straw-white hull and white pericarp(Fig.5).Use of pericarpspecific Kala4 and hull-specific S1 contributed to the breeding of‘‘purple rice”and‘‘purple hull”cultivars.The hull-specific S1 must act together with C1 and A1 to ensure the hull-specific accumulation of purple color(Fig.5).

7.Reduced grain dormancy

Grain dormancy is another domestication trait[128].Wild rice generally exhibits deeper dormancy than cultivated rice.Deep dormancy of wild rice grains leads to desynchronizing germination,which is beneficial for the survival and propagation of wild rice.For cultivated rice,weak dormancy and uniform germination are favored.However,too-weak dormancy can lead to pre-harvest sprouting,impairing grain quality and yield.Thus,moderate dormancy is desirable for cultivated rice.A series of genes regulating grain dormancy have been identified[129-131],a few of which have been found to be domesticated genes.

The G gene,which is involved in regulating seed coat color and seed dormancy in soybean,has been subjected to parallel selection during the domestication of multiple crops[132].OsG,the rice ortholog of G,also controls grain dormancy.Overexpression of OsG increases and knockout of OsG reduces grain dormancy.Genome-wide selection analysis showed that OsG is located in a selective region.In most cultivated but not in wild accessions,a SNP located in the conserved C-terminal region of OsG,was fixed.Given that the OsG allele of wild rice is stronger than that of cultivated rice in increasing grain dormancy,the selection of Osg contributed to reduced grain dormancy in cultivated rice.

Sdr4(Seed dormancy 4)is associated with a major QTL for grain dormancy in Asian rice[133].Loss of function of Sdr4 results in complete loss of dormancy.OsVP1(Oryza sativa viviparous-1)promotes the expression of Sdr4[133].Knockout of OsVP1 also leads to reduced grain dormancy[133,134].All tested geng accessions harbor the weak-dormancy allele of Sdr4,whereas both the strong and weak-dormancy alleles are widely distributed in tested xian accessions.The weak-dormancy allele of Sdr4 is not found in Asian wild rice,suggesting that it arose during domestication.

Besides OsG1 and Sdr4,the Green Revolution gene OsGA20ox2 is involved in grain dormancy regulation[135].However,in contrast to OsG1 and Sdr4,OsGA20ox2 suppresses grain dormancy,and thus the natural semidwarf alleles of OsGA20ox2 increase grain dormancy.

8.Improved regional adaptability

Compared with the limited distribution area of wild rice,the planting area of cultivated rice has greatly expanded.The improved regional adaptability of cultivated rice is due mainly to adaptation to different temperatures and day lengths.Several genes contributing to the improved regional adaptability of cultivated rice have been identified.They are involved in cold tolerance,heat tolerance,and heading date regulation.

COLD1(CHILLING-TOLERANCE DIVERGENCE 1)corresponds to a QTL for cold tolerance in the seedling stage[136].COLD1 encodes a GTPase-accelerating protein with nine transmembrane domains.COLD1 interacts with and activates theαsubunit of G protein(Gα),thereby activating a temperature-sensing Ca2+channel.The coldtolerance allele of COLD1 harbors a nonsynonymous SNP that increases the ability of COLD1 to activate Gαand increases cold tolerance.Cultivated accessions carrying the cold-tolerance allele of COLD1 are distributed mainly in regions with lower yearly temperatures,such as the northern areas of China,Japan,and the Republic of Korea.Accessions grown in regions of higher yearly temperatures generally do not carry the cold-tolerance allele of COLD1.Phylogenetic analysis showed that this allele was already present in wild rice and was selected during the breeding of geng rice.CTB4a(Cold tolerance at booting stage 4a),which encodes a leucine-rich repeat receptor-like protein kinase,contributes to cold adaptation in the booting stage[137].CTB4a positively regulates cold tolerance in a dosage-dependent manner.Natural variations in the promoter region of CTB4a affect its expression and lead to differing levels of cold tolerance.As with COLD1,accessions grown in regions with lower yearly temperatures carry the cold-tolerance allele of CTB4a,which was artificially selected during the breeding process of temperate geng rice.Besides COLD1 and CTB4a,natural variations in bZIP73,qLTG3-1(a QTL for low-temperature germinability on chromosome 3),LTG1(Low Temperature Growth 1),Ctb1(Cold tolerance at booting stage 1),and OsLTPL159 are also involved in cold-tolerance regulation[138-141].bZIP73 encodes a bZIP transcription factor,and a functional SNP in bZIP73 increases the cold tolerance of geng rice[142].qLTG3-1 encodes a plant-specific protein with unknown function and regulates low temperature germinability[141].LTG1 encodes a CKI(casein kinase I),and a nonsynonymous SNP in LTG1 is associated with growth rate under low temperature[139].Ctb1,which encodes an F-box protein,is involved in regulating booting-stage cold tolerance[140].OsLTPL159 encodes a nonspecific lipid transfer protein and regulates cold tolerance in the seedling stage[138].

African cultivated rice grows under higher-temperature environments than Asian cultivated rice.TT1(Thermo-tolerance 1)is a major QTL accounting for the difference in heat tolerance between Asian and African cultivated rice[143].TT1 encodes anα2 subunit of the 26S proteasome[143].African cultivated rice carries the heat-tolerance allele of TT1(OgTT1),and the protein encoded by OgTT1 is more efficient at eliminating the heat stress-induced cytotoxic denatured proteins and consequently confers higher heat tol-erance[143].Natural variations of TT1 in the Asian rice population lead to differing expression levels of TT1,and the frequency of highly expressed TT1 allele decreases with climatic temperature[143],suggesting that TT1 also contributes to differences in heat tolerance in the Asian rice population.Thus,different TT1 alleles were selected for adaptation to different climatic temperatures.

Fig.6.Characters differing between wild rice and modern cultivars.Seven characters distinguishing wild rice and modern cultivar are shown,and genes contributing to these changes during rice domestication and improvement are listed.

Rice is a short-day plant,and photoperiod largely determines its heading date.Adaptation to long photoperiods at high latitudes also contributed to the improved regional adaptation of cultivated rice.Molecular mechanisms underlying heading date control have been well studied,and genes for several QTL for photoperiod response and heading date have been cloned[144].These include Hd1[145],Ghd7.1/OsPRR37/DTH7[146-148],Hd3a[149],Hd17[150],Ghd7[151],Ghd8/DTH8/LHD1[152-154],Hd6[155],Hd16/EL1[156,157],DTH3[158],Hd18[159],DTH2[160],Ehd1[161],Ehd4[162],and Ef-cd[163].Combination of different alleles of these genes could result in different flowering times under distinct photoperiods[164,165].

9.Conclusions and perspectives

Plant architecture,awn characteristics,shattering ability,grain color,grain dormancy,panicle architecture,and regional adaptability have been altered during the transition from wild rice to landraces and then to modern cultivars during rice domestication and improvement(Fig.6).Though some genes contributing to rice domestication and improvement have been identified,the detailed regulatory mechanisms and molecular network in which they function are still largely unknown.Their elucidation would reveal much about rice domestication.

In fact,there are still other differences between cultivated and wild rice,including grain quality,stigma exsertion,uniformity of flowering,self-incompatibility,nutrition uptake,plant height,and disease resistance.Several genes regulating grain quality and nutrition uptake have been identified.For example,natural variations in Waxy,Chalk5(Grain chalkiness 5),TOND1(Tolerance Of Nitrogen Deficiency 1),and NRT1.1B(Nitrate-transporter 1.1B)contribute respectively to differences in amylose content,chalkiness,tolerance to nitrogen deficiency,and nitrate uptake[166-171].Compared with wild rice,the genetic diversity of cultivated rice is greatly reduced owing to the domestication bottleneck[11,172-175].Thus,some beneficial genes or alleles carried by wild rice have been lost during the process of domestication.Further identification of these ‘‘missing”beneficial genes/alleles would provide promising genetic resources for rice breeding.

Asian cultivated rice(O.sativa L.)and African cultivated rice(O.glaberrima)were separately domesticated from the wild species O.rufipogon and O.barthii.Currently,intense research effort is focused on Asian rice owing to its importance for worldwide food,whereas studies in African rice are relatively few and the genetic mechanisms underlying its domestication are still largely unknown.Further investigation of the domestication mechanisms of African rice will afford a basis for comparison of the domestication and improvement processes in these two cultivated rice species,contributing to further understanding of the nature of domestication and to the development of new cultivars by combining favorable alleles from Asian and African rice.

The Oryza genus consists of 27 species,and only two AA genome type wild species,O.rufipogon and O.barthii,were domesticated to cultivated rice species[1-3].A recent study established a route for de novo domestication and improvement of the tetraploid wild rice O.alta(CCDD)[176],showing the feasibility of‘‘creating”new cultivated rice species and opening a new era of rice domestication and improvement.Along with the rapid development of genomeediting technology and gradual increase in knowledge about rice domestication and improvement,‘‘creating”new cultivated rice species by de novo domestication of wild Oryza species with other genome types would expand human food resources.

CRediT authorship contribution statement

Chuanqing Sun and Ran Xuconceived the outline of the manuscript,Ran Xudrafted the manuscript,Chuanqing Suncritically revised the manuscript.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

We thank Dr.Kun Zhang and Dr.Yuanjie Li for their help in preparing Fig.1.This work was supported by the National Natural Science Foundation of China(31830065 and 31960159).We apologize to colleagues whose work is not covered in this review owing to space limitation.