Jifeng Zhu,Jing Wu,Lnfen Wng,Mtthew W.Blir,Zhendong Zhu,Shumin Wng,*

aInstitute of Crop Science，Chinese Academy of Agricultural Sciences，Beijing 100081，China

bDepartment of Agriculture&Environment，Tennessee State University，Nashville，TN，USA

QTL and candidate genes associated with common bacterial blight resistance in the common bean cultivar Longyundou 5 from China

Jifeng Zhua,Jing Wua,Lanfen Wanga,Matthew W.Blairb,Zhendong Zhua,Shumin Wanga,*

aInstitute of Crop Science，Chinese Academy of Agricultural Sciences，Beijing 100081，China

bDepartment of Agriculture&Environment，Tennessee State University，Nashville，TN，USA

A R T I C L E I N F O

Article history：

28 June 2016

Accepted 7 July 2016

Available online 22 July 2016

Common bean（Phaseolus vulgaris L.）Common bacterial blight

Quantitative trait locus

Days after inoculation

Common bacterial blight（CBB），caused byXanthomonasaxonopodis pv.phaseoli andXanthomonas fuscans subsp.fuscans（Xff），is a worldwide disease of common bean（Phaseolus vulgaris L.）. Longyundou 5，a Chinese cultivar in the Mesoamerican gene pool of common bean，displays resistance to the Xff strain XSC3-1.To identify the genetic mechanisms behind this resistance，we crossed Long 5 with a susceptible genotype to develop a mapping population of F2plants. PlantresistancetoCBBwasidentifiedat14and21 daysafterinoculationwithXffstrainXSC3-1. A major QTL at 14 and 21 days after inoculation was mapped on chromosome Pv10 with LOD scores of 6.41 and 5.35，respectively.This locus was associated with SAP6，a previouslyidentifiedand much-used dominant marker，but in a 4.2 cM interval between newcodominant markers BMp10s174 and BMp10s244.Ten candidate genes were found between markers

BMp10s174 and BMp10s244 on chromosome Pv10 and could encode defense response proteins respondingto CBB pathogens.Four pairseach of epistatic QTL for CBB resistance weredetected at 14 and 21 days after inoculation.Phenotypic variation explained by the epistatic QTL ranged from7.19%to12.15%and7.72%to8.80%at14and 21 daysafterinoculation，respectively.These results confirmedthe importance of epistasis in CBB resistance in common bean.The adjacent markers found may be more efficient for marker assisted selection in common bean breeding for CBB resistance owing to their closer linkage to the target QTL.

?2016 Crop Science Society of China and Institute of Crop Science，CAAS.Production and hosting by Elsevier B.V.This is an open access article under the CC BY-NC-ND license

（http://creativecommons.org/licenses/by-nc-nd/4.0/）.

1.Introduction

Common bean（Phaseolus vulgaris L.）is one of the most important legumes on earth and provides many nutrients，high levels of proteins，unique carbohydrates，and essential vitamins for millions of people worldwide［1］.The annual production of dry beans is approximately 25 million tons，representing over half of the world's total food legume output in 2014［51］.However，the production of common bean is limited by many plant diseases，such as halo blight，angular leaf spot，and CBB［2］.Of these，CBB is responsible for yield losses of 20%-60%in susceptible cultivars，especially under environmental conditions favoring disease［3］.

CBB is a seedborne disease caused by Xap or Xff［4］and occurs at any developmental stage of bean［5］.The two variants have the same host range and epidemiological features and show similar biochemical phenotypes，except that Xff colonies produceabrownpigmentationinmedia［6］.However，studiesof host-pathogen interactions have shown that these pathogens vary in their virulence and prevalence in the two gene pools of common bean［7-9］.Most commonly，Xap is associated with CBB in large-seeded bean cultivars of the Andean gene pool，whereas Xff is associated with CBB in both Andean and Mesoamerican bean cultivars［8］.In addition，Xff strains appear to be more pathogenic towards their hosts than Xap strains［7］. In China，common beans are cultivated mainly in the northern region of Heilongjiang province，where CBB is a severe and destructive disease.Two small-seeded bean cultivars（Long 5 and Long 4）of the Mesoamerican gene pool are the leading varietiesinHeilongjiang.Theblack-seededLong4issusceptible to CBB，whereas the white-seeded Long 5 is resistant.Pathogen strains isolated from diseased samples of Long 4 in this region were identified as Xff by our laboratory.

Genetic disease resistance is the most biologically safe，sociallyacceptable，effective，and environmentally friendlyway to control bacterial，fungal，and viral plant pathogens［10］. Molecular markers for disease resistance are powerful tools for analyzing the genome and are comprehensively applied in mapping genes and MAS［11］.To date，24 QTL conferring resistance to CBB have been identified，distributed across all 11 chromosomes of common bean［2，12-15］.Among these loci，most have been tagged with SCAR markers.Examples include BC420［13，16］，SU91［17］，and SAP6［5，18］，which are linked with three major QTL of particular interest to researchers in CBB resistance［5，9-12，15，19，20］.

BC420 is located on chromosome Pv06［12］and is thought to be derived only from tepary bean（Phaseolus acutifolius）via the breeding line XAN159［21］.This locus accounted for 62%-63%of phenotypic variation for CBB resistance［16，22］.Upon mapbased characterization，21 novel genes were predicted in this region，among which BC420-CGs10 and BC420-CGs14 showed strong associations with CBB resistance［20］.Another QTL of importance in conditioning resistance to CBB from XAN159 is the SCAR marker SU91［17］，located on chromosome Pv08 in at least one study to date［12］.This locus explained 14%-17%of phenotypic variation for CBBresistance［10］.Sixteen geneshave been identified as linked to this locus by a map-based cloning approach，amongwhichSU91-CGs10andSU91-CGs11presented strong associations with CBB resistance［20］.A third QTL linked to SAP6 has been found in the Mesoamerican common bean gene pool，derived from the great northern landrace cultivar Montana No.5，and was located on chromosome Pv10［5］.The presence of this locus accounted for 35%of the variation for resistance to CBB in an F2population derived from the cross of Montana No.5（resistant）with Othello（susceptible）［5］.

In recent years，BC420，SU91，and SAP6 have been widely used in MAS of common bean despite being dominant markers［11，12，16］.For example，the breeding line HR67 was selected for CBB resistance based on BC420［3］，while ABCP-8 pyramided two QTL based on SU91 and SAP6［23］.Researchers have developed codominant markers to replace BC420 and SU91［20］；but no new codominant markers have been developed for SAP6 and these codominant markers have not been tested for their efficiency in MAS for CBB resistance.

Considering the less codominant markers have been developed in MAS for CBB resistance，our objective in this study was to identify QTL controlling CBB resistance in a cross between the two modern cultivars Long 5×Long 4.A detailed understanding of resistance in Long 5 will help breeders use this resistant parent to improve future cultivars.The new Xff strain from Heilongjiang was selected to investigate the phenotype of CBB resistance in this study because of its prevalence and because most previous studies have used the Xap strain to study the inheritance of the trait.Another novel aspect of this study was the use of many codominant markers rather than previously developed RAPD-derived markers for the analysis of CBB resistance.Careful physical mapping of multiple CBB resistance loci from Long 5 is useful for the dissection of new genes involved in pathogenicity and plant response.We also developed and genetically mapped new codominant SSR markers that could be used to replace older SCAR markers for MAS.The finding of multiple QTL in the Long 5 variety is useful for breeding within the white-seeded commercial class or across other Mesoamerican and possibly Andean seed types.

2.Materials and methods

2.1.Plant materials

The parents used for developing the population were Long 5（resistant）and Long 4（susceptible）（Fig.1）.Long 5，a dry bean with small white seeds，used as the male，was developed from a cross between Dabaidou and B-7150 and is widely cultivated in Heilongjiang Province，China.The Long 5×Long 4 hybrids were advanced from the F1generation by selfing to yield an F2population comprising 803 individuals for fine mapping of CBB resistance.All of the plants were grown in plastic pots（23 cm×18 cm×18 cm）under a 14 h/10 h photoperiod at 25°C（day）and 20°C（night）in a greenhouse in Beijing，China.

2.2.Inoculation and phenotypic evaluation of CBB

The Xff strain identified as XSC3-1 was isolated from CBB-infected samples in the Heilongjiang Province of China and was used for phenotypic evaluation of the F2population and parental controls.Pathogenic bacteria were selected on Milk Tween agar medium for 4-5 days at 28±2°C［24］，after whichcolonies were transferred to nutrient broth liquid culture medium incubated with shaking for 48 h（200 r min-1，28± 2°C）.The bacterial cells were diluted to 1×108CFU mL-1with sterile distilled water before inoculation.Long 5，Long 4 and the F2individuals with fully expanded first trifoliate leaves were inoculated using the needle method［25］.The reaction to the pathogen was evaluated on a scale of 1 to 10 based on the description of Zapata et al.［19］at 14 and 21 DAI when symptoms were present.

Fig.1-Phenotypes of Long 5 and Long 4 inoculated with Xff strain XSC3-1.

2.3.Genotyping using SSR markers

Genomic DNA was extracted from young leaves using a modified cetyltrimethylammonium bromide method［26］.A set of 381 SSR markers including ATA，BM，BMc，BMd，BMg，GATS，PVBR，PVM，PSSR，and PV from the BIC website（http:// bic.css.msu.edu/_pdf/Bean_SSR_Primers_2007.pdf）or a recent report［27］，and 2805 SSR markers named BMpnsX，mined from the whole-genome sequence［28］were used to construct a linkage map.The new SSR markers were designed with SSR Locator［29］based on the following parameters:size of the expected PCR amplification products，100-280 bp；primer size，15-25 bp；annealing temperature，50-65°C；and optimum G/C content，50%.The newly developed markers were named BMpnsX markers，in which BMp represents Bean Microsatellite from the physical sequence of common bean，the number“n”indicates the chromosome，and“X”represents a numerical code for the newly designed marker.

PCR amplification was performed in 15-μL volumes containing 20 ng of template DNA，0.2 μmol L-1forward and reverse primers each（Invitrogen，USA），0.25 mmol L-1dNTPs，1.5 μL of 10×Taq buffer with 1.5 mmol L-1Mg2+，and 1 U of Taq DNA polymerase in a T100 Thermal Cycler（Bio-Rad Research，USA）.The PCR thermocycling conditions were 95°C for 5 min，followed by 35 cycles of 95°C for 30 s，54°C for 45 s，and 72°C for 45 s；and a final extension of 5 min at 72°C.The PCR products were separated on 8%nondenaturing polyacrylamide gels.

2.4.Linkage and QTL analysis A genetic linkage map of the F2population was constructed using the MAP functionality in QTL IciMapping version 4.0［30］.A LOD score of 3.0 was used as a linkage threshold and a recombination frequency value of 0.30.The linkage map was constructed with genetic distances（cM）calculated using the Kosambi mapping function［31］.Linkage groups were named based on the chromosome information of the genomic sequence［28］.

QTLweredetectedusingBIPfunctionalityinQTL IciMapping.ICIM-ADD and ICIM-EPI were selected as mapping methods［32］.The mapping parameters of each step for ICIM-ADD and ICIM-EPI were set at 1.0 cM and 5.0 cM，respectively，and a probability of 0.05 in stepwise regression was selected for each mapping method.The LOD thresholds of ICIM-ADD and ICIM-EPI were set at 3.0 and 5.0，respectively，to claim significance.Identified QTL were designated by the letter q followed by CBB and then the chromosome number.

2.5.Gene analysis

Functional annotation was performed based on the common bean whole genome sequence［28］.Association analyses between SSR markers around the target region and CBB severity were performed with TASSEL 2.1 using the general linear model method［33］.

3.Results

3.1.Comparison of CBB resistance levels of parents

Based on preliminary screening experiments，we selected one resistant genotype（Long 5）and one susceptible genotype（Long 4）for further study（Fig.1）.In the screening，Long 5 exhibited excellent resistance to CBB，with mean phenotypic resistance scores of 2.4 and 3.6 at 14 and 21 DAI，respectively. In contrast，the Long 4 genotype showed high susceptibility，with the inoculated side of the leaf becoming necrotic and the disease progressing to the uninoculated（control）side of the leaf at 14 and 21 DAI.

Based on these results，the two genotypes（Long 5 and Long 4）were chosen to construct a segregating population for an inheritance study of Xff resistance（Figs.S1，2）.The F2population showed pronounced variation and segregation of CBB resistance or susceptibility.The distribution of CBB resistance was continuous and approximately normal in the F2generation at 14 and 21 DAI，indicating the quantitative inheritance of the trait.

3.2.Genetic linkage and map construction

A total of 228 polymorphic markers including 50 previously discovered and 178 new markers were genotyped in twoparents.Thepolymorphismproportion（13.12%）ofthe previously discovered markers was higher than that of the new markers（6.35%）.Linkage analysis was performed using 803 F2individuals and 228 loci（Fig.S2）.The total length of the linkage map was 1597.79 cM with an average genetic distance of 7.83 cM between adjacent markers.This analysis resulted in the formation of 12 linkage groups with locus numbers ranging from three to 33.The order of loci for each linkage group and correspondences among the 12 linkage groups obtained for the 11 bean chromosomes were established except for chromosome Pv03，which was divided into two linkage groups（3a and 3b）owing to insufficient marker density.

Fig.2-Frequency distribution of disease scores in an F2population screened for resistance to Xff strain XSC3-1.

3.3.Major QTL for CBB resistance in Long 5

A total of six putative QTL with additive effects were identified at14and21 DAI（Table1）.FourminorQTLweredetectedontwo different chromosomes，qCBB8-1 and qCBB8-2 on chromosome Pv08 at 14 DAI and qCBB6-1 and qCBB6-2 on chromosome Pv06 at 21 DAI.Notably，qCBB10-1，with the highest effect，was identified on another chromosome（Pv10）at 14 and 21 DAI（Table 1，F(xiàn)ig.3-B），explaining 4.29%of phenotypic variation at 14 DAI and 3.56%at 21 DAI.qCBB10-1 was flanked by the two markers BMp10s174 and BMp10s244 within an approximately 271.9-kbregionlocatedbetweenthe39，730，677 bpand 40，002，585 bp of G19833 on chromosome Pv10（Fig.4-A）.

To select the best marker for MAS，we further evaluated the association of markers around qCBB10-1 with CBB severity in this population（Table 2）.As a result，five and four SSR markers were significantly（P≤0.05）associated with CBB score at 14 and 21 DAI，respectively.Markers BMp10s243 and BMp10s244 were highly associated with CBB score（P≤0.001）at 14 DAI，whereas only BMp10s244 was highly associated with CBB score（P≤0.001）at 21 DAI.These results showed that marker BMp10s244 was tightly linked with CBB resistance and would be an effective marker for molecular breeding.

3.4.Annotation and candidate gene prediction for qCBB10-1 region

Based on G19833 annotation information，25 predicted genes were located in this region（Fig.4-B）.Ten of these predicted genes encode proteins associated with plant defense response to pathogens:Phvul.010G128100 encoding an NDPK；Phvul. 010G128800 encoding a LOX；Phvul.010G128900 encoding a CYPs；Phvul.010G129000 encoding a PKc-like protein；Phvul. 010G129100encodingaRelA/SpoT-likeprotein；Phvul. 010G129400 encoding a GRAS protein；and Phvul.010G129600，Phvul.010G129700，Phvul.010G129800，and Phvul.010G129900 encoding CLP（Table 3）.The functions of the remaining predicted genes may be unrelated to disease resistance，as they encode proteins such as transmembrane receptor protein，small nuclear ribonucleoprotein，and ubiquitin ligase protein.

Table 1-Statistics of QTL for CBB resistance identified at 14 and 21 DAI.

3.5.Epistatic QTL for CBB resistance in Long 5

Epistatic effects play a crucial role in inheritance of complex traits，especially plant resistance to disease［34］.We also detected epistatic QTL for CBB.Four pairs of epistatic QTL each were identified at 14 and 21 DAI and associated with 10 marker intervals（Table S1）.These epistatic QTL were distributed on chromosomes Pv01，Pv06，Pv08，Pv09，and Pv11，and explained 7.19%-12.15%of phenotypic variance at 14 DAI and 7.72%-8.80%at 21 DAI.The interactions among qCBB8-3，qCBB10-2，and qCBB11-1 were identified at both 14 and 21 DAI with strong effects of additive interaction（0.89-1.37），but the directions of interaction were different at the two evaluation dates.The QTL pairs on chromosome Pv06（qCBB6-3/qCBB6-3 at 14 DAI and qCBB6-4/qCBB6-5 at 21 DAI）showed high DA or AD interactions，although the DA and AD effects were in different directions.qCBB6-3/qCBB6-3 at 14 DAI also showed high DD interaction（-1.49）.The highest DD interactions were found at 21 DAI between qCBB9-1 and qCBB11-1（-6.40）and between qCBB8-3 and qCBB11-1（5.34）.These epistatic QTL merit further study.

Fig.3-Mapping of QTL for CBB resistance in F2population derived from Long 4×Long 5.A，Chromosome Pv10 of an F2population derived from Long 4×Long 5.At left are map interval sizes in Kosambi centiMorgan（cM）units and at right are listed markers.B，The LOD score of qCBB10-1 for CBB resistance at 14 and 21 DAI.

4.Discussion

CBB，caused by Xap and Xff［4］，is one of the main constraints to common bean production in most countries［2］.Many studies havefounditsresistancetobeinheritedquantitativelyviaafew major genes［14，22］.To date，approximately 24 CBB resistance loci on all 11 chromosomes of common bean have been reported，mostly as QTL［12，15］.Among these loci，five QTL have been located on chromosome Pv07［18，22，35］.In contrast，only one QTL each has been identified on chromosomes Pv01［35］，Pv04［13］，Pv06［13，16］，and Pv10［5，18，35］.One important locus，SAP6-QTL［5］wasfoundbetween39，938，699and 39，939，569 bp on chromosome Pv10［36］.In the present study，qCBB10-1wasflankedbySSRmarkersBMp10s174and BMp10s244 on chromosome Pv10 located very precisely at nucleotide positions 39，730，677 and 40，002，585 bp in G19833. Theseflankingmarkersprovidecodominantmarkersandallow fine mapping and isolate dissection to reduce linkage drag around the frequently used SAP6.This was previously impossible with the original SAP6 marker，which is dominant and not as highly reproducible as the SSR markers.In addition，the new markers will be useful for map-based gene cloning of the CBB resistance locus，which has eluded discovery when the simple SCAR marker alone was used［5，18，35］.Given that the target region of qCBB10-1 contained the SAP6 marker sequence，qCBB10-1 may be located at the position（SAP6）previously identified.But ina novel twist，thegenesfound inthe candidate regionandthelikelydiseasepathway-associatedgenes discovered in the present study are likely candidates for the resistance R gene itself.

Fig.4-Candidate genes associated with CBB resistance in the qCBB10-1 region.A，physical positions of some markers located around qCBB10-1（in red）.At left are listed markers and at right are physical positions in base pairs（bp）.B，predicted candidate genes for CBB resistance and locus names of candidate genes at right according to http：//www.phytozome.net/.

Table 2-Testing of association of SSR markers around qCBB10-1 with CBB severity.

The additive and epistatic nature of the now better-defined CBB resistance gene on chromosome Pv10 is important to emphasize.Gene interactions in the coordination of resistance gene pathways may explain epistasis in large mapping populations，where the detection of these effects is easier than in small populations.In our analysis of an 803-plant population，we found epistasis between Pv10 loci and other loci on Pv08 and Pv11 to be important for CBB resistance. These results agree with those of Vandemark et al.［10］，who identified recessive epistatic interactions between the BC420 and SU91 tagged loci for resistance to the Xap pathogen. Epistasis typically plays a strong role in quantitative characters［34］，but its effects on CBB resistance have not yet been characterized.

Torecapitulatethephysicalmappingbasedonthe annotation of the genome sequence［28］，25 genes were predicted to lie in the qCBB10-1 region and 10 of these predicted genes encoded proteins involved in defense mechanisms against pathogens（Table 3）.These genes included NDPK，PKc-like，LOX，CYP，RelA/SpoT-like，GRAS，and GLP，which belong to PK，lipase and GLP，etc.Among these proteins，the PK superfamily contains many typical PKs broadly associated with plant disease response［37，38］.NDPK and PKc-like proteins are an important type of PK that play dynamic roles in enhancing tolerance of plants against pathogen infections such as bacterial blight disease of rice［37-40］.Similarly to PK，LOX，CYP，GLP，and RelA/SpoT-like protein also involve in defense-responsive or defense-related against pathogen attack in crops［41-46］.For example，GLP regulates plant disease resistance through its OxO，SOD，AGPPase，or PPO enzymatic properties［45，46］.However，this is the first detailed description of candidate genes around the qCBB10-1/SAP6 locus.These annotations of candidate genes provide basic information for cloning SAP6 genes and elucidating the resistance mechanism of CBB.

Table 3-Gene annotation of the qCBB10-1 region.

DNA markers tightly linked to target genes can be used as molecular tools for MAS in crops［47］，such as rice［48］，maize［49］，and wheat［50］.The most widely used markers in majorcrops are SSR or various SNP assays because they are highly reliable，codominant in inheritance，relatively simple and inexpensive touse，andgenerally polymorphic［47］.In common bean，a type of sequence-tagged site marker，the SCAR，derived from specific DNA sequences of markers（such as RAPDs）has been widely used for MAS［47］of bean breeding despite its disadvantages in germplasm specificity，sensitivity to DNA quality，and dominant nature.It is necessary to transition from SCAR markers in common bean to SSR markers for fine mapping and MAS.Our study is an example of such a transition.

The major SCAR markers used for MAS of CBB resistance are BC420，SU91，and SAP6［12，23］.As SCARs are dominant markers that cannot distinguish heterozygous from homozygous loci，Shi et al.［20］developed the codominant candidate gene markers BC420-CG14 and SU91-CG11 to replace BC420 and SU91 for MAS.However，for SAP6-QTL，no codominant markers have been developed or could be used efficiently in MAS.In our study，SSR marker BMp10s244 was identified as showing strong association with CBB resistance in Long 5 and its tightly linked QTL was mapped to the SAP6-QTL using physical positions of G19833.This marker may replace SAP6 in MAS for CBB resistance.

Acknowledgments

This study was supported by the National Natural Science Foundation of China（31471559），the China Agriculture Research System（CARS-09），the National Key Technology R&D Program of China（2013BAD01B03-18a），the Evans Allen Fund of the U.S.Department of Agriculture，and the Agricultural Science and Technology Innovation Program （ASTIP）of the Chinese Academy of Agricultural Sciences.

Supplementary data

Supplementary data for this article can be found online at http://dx.doi.org/10.1016/j.cj.2016.06.009.

R E F E R E N C E S

［1］E.Bitocchi，L.Nanni，E.Bellucci，M.Rossi，A.Giardini，P.S. Zeuli，G.Logozzo，J.Stougaard，P.McClean，G.Attene，R.Papa，Mesoamerican origin of the common bean（Phaseolus vulgaris L.）is revealed by sequence data，Proc.Natl.Acad.Sci.U.S.A. 109（2012）E788-E796.

［2］S.P.Singh，H.F.Schwartz，Breeding common bean for resistance to diseases:a review，Crop Sci.50（2010）2199-2223.

［3］M.Lema-Marquez，H.Teran，S.P.Singh，Selecting common bean with genes of different evolutionary origins for resistance to Xanthomonas campestris pv.phaseoli，Crop Sci.47（2007）1367-1374.

［4］M.L.Schuster，D.P.Coyne，Biology，epidemiology，genetics and breeding for resistance to bacterial pathogens of Phaseolus vulgaris L.Hortic.Rev.3（1981）28-58.

［5］P.N.Miklas，D.Coyne，K.F.Grafton，N.Mutlu，J.Reiser，D. Lindgren，S.P.Singh，A major QTL for common bacterial blight resistance derives from the common bean great northern landrace cultivar Montana No.5，Euphytica 131（2003）137-146.

［6］P.H.Goodwin，C.R.Sopher，Brown pigmentation of Xanthomonas campestris pv.phaseoli associated with homogentisic acid，Can.J.Microbiol.40（1994）28-34.

［7］N.Mutlu，A.K.Vidaver，D.P.Coyne，J.R.Steadman，P.A. Lambrecht，J.Reiser，Differential pathogenicity of Xanthomonas campestris pv.phaseoli and X.fuscans subsp. fuscans strains on bean genotypes with common blight resistance，Plant Dis.92（2008）546-554.

［8］R.W.Duncan，S.P.Singh，R.L.Gilbertson，Interaction of common bacterial blight bacteria with disease resistance quantitative trait loci in common bean，Phytopathology 101（2011）425-435.

［9］D.M.Viteri，S.P.Singh，Response of 21 common beans of diverse origins to two strains of the common bacterial blight pathogen，Xanthomonas campestris pv.phaseoli，Euphytica 200（2014）379-388.

［10］G.J.Vandemark，D.Fourie，P.N.Miklas，Genotyping with real-time PCR reveals recessive epistasis between independent QTL conferring resistance to common bacterial blight in dry bean，Theor.Appl.Genet.117（2008）513-522.

［11］P.D.O'Boyle，J.D.Kelly，W.W.Kirk，Use of marker-assisted selection to breed for resistance to common bacterial blight in common bean，J.Am.Soc.Hortic.Sci.132（2007）381-386.

［12］P.N.Miklas，J.D.Kelly，S.E.Beebe，M.W.Blair，Common bean breeding for resistance against biotic and abiotic stresses:from classical to MAS breeding，Euphytica 147（2006）105-131.

［13］B.Tar'an，T.E.Michaels，K.P.Pauls，Mapping genetic factors affecting the reaction to Xanthomonas axonopodis pv.phaseoli in Phaseolus vulgaris L.under field conditions，Genome 44（2001）1046-1056.

［14］S.Liu，K.F.Yu，S.J.Park，Development of STS markers and QTL validation for common bacterial blight resistance in common bean，Plant Breed.127（2008）62-68.

［15］C.Shi，A.Navabi，K.F.Yu，Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations，BMC Plant Biol.11（1）（2011）52.

［16］K.F.Yu，S.J.Park，V.Poysa，Marker-assisted selection of common beans for resistance to common bacterial blight: efficacy and economics，Plant Breed.119（2000）411-415.

［17］F.Pedraza，G.Gallego，S.Beebe，J.Tohme，Marcadores SCAR y RAPD para la resistencia a la bacteriosis comun（CBB），Taller de Mejoramiento de Frijol Para el Siglo XXI:Bases para una Estrategia para America Latina，CIAT，Cali，Colombia 1997，pp.130-134.

［18］P.N.Miklas，V.Stone，M.J.Daly，J.R.Stavely，J.R.Steadman，M.J. Bassett，R.Delorme，J.S.Beaver，Bacterial，fungal，and viral disease resistance loci mapped in a recombinant inbred common bean population（‘Dorado'/XAN 176），J.Am.Soc. Hortic.Sci.125（2000）476-481.

［19］M.Zapata，J.S.Beaver，T.G.Porch，Dominant gene for common bean resistance to common bacterial blight caused by Xanthomonas axonopodis pv.phaseoli，Euphytica 179（2011）373-382.

［20］C.Shi，K.F.Yu，W.L.Xie，G.Perry，A.Navabi，K.P.Pauls，P.N. Miklas，D.Fourie，Development of candidate gene markers associated to common bacterial blight resistance in common bean，Theor.Appl.Genet.125（2012）1525-1537.

［21］C.V.Thomas，J.G.Waines，F(xiàn)ertile backcross and allotetraploid plants from crosses between tepary beans and common beans，J.Hered.75（1984）93-98.

［22］K.F.Yu，S.J.Park，B.L.Zhang，M.Haffner，V.Poysa，An SSR marker in the nitrate reductase gene of common bean is tightly linked to a major gene conferring resistance to common bacterial blight，Euphytica 138（2004）89-95.

［23］N.Mutlu，P.N.Miklas，J.R.Steadman，A.M.Vidaver，D.T. Lindgren，J.Reiser，D.P.Coyne，M.A.Pator-Corrales，Registration of common bacterial blight resistant pinto bean germplasm line ABCP-8，Crop Sci.45（2005）806-807.

［24］J.W.Sheppard，C.Kurowski，P.M.Remeeus，International Rules for Seed Testing，7-021:Detection of Xanthomonas axonopodis pv.phaseoli and Xanthomonas axonopodis pv. phaseoli var.fuscans on Phaseolus vulgaris，International Seed Testing Association（ISTA），Bassersdorf，Switzerland，2007.

［25］M.Zapata，Proposed of a uniform screening procedure for the evaluation of variability of Xanthomonas axonopodis pv. phaseoli and resistance on leaves of Phaseolus vulgaris under greenhouse conditions，Annu.Rep.Bean Improv.Coop.49（2006）213-214.

［26］L.K.Afanador，S.D.Hadley，J.D.Kelly，Adoption of a“mini-prep”DNA extraction method for RAPD marker analysis in common bean（Phaseolus vulgaris L.），Annu.Rep. Bean Improv.Coop.36（1993）10-11.

［27］M.L.Chen，J.Wu，L.F.Wang，X.Y.Zhang，M.W.Blair，J.Z.Jia，S.M.Wang，Development of mapped simple sequence repeat markers from common bean（Phaseolus vulgaris L.）based on genome sequences of a Chinese landrace and diversity evaluation，Mol.Breed.33（2014）489-496.

［28］J.Schmutz，P.E.McClean，S.Mamidi，G.A.Wu，S.B.Cannon，J. Grimwood，J.Jenkins，S.Shu，Q.Song，C.Chavarro，M.Torres-Torres，V.Geffroy，S.M.Moghaddam，D.Gao，B.Abernathy，K. Barry，M.Blair，M.A.Brick，M.Chovatia，P.Gepts，D.M. Goodstein，M.Gonzales，U.Hellsten，D.L.Hyten，G.Jia，J.D. Kelly，D.Kudrna，R.Lee，M.M.Richard，P.N.Miklas，J.M. Osorno，J.Rodrigues，V.Thareau，C.A.Urrea，M.Wang，Y.Yu，M.Zhang，R.A.Wing，P.B.Cregan，D.S.Rokhsar，S.A.Jackson，A reference genome for common bean and genome-wide analysis of dual domestications，Nat.Genet.46（2014）706-713.

［29］L.C.Maia，D.A.Palmieri，V.Q.Souza，W.M.Kopp，F(xiàn).I.Carvalho，A.C.Oliveira，SSR locator:tool for simple sequence repeat discovery integrated with primer design and PCR simulation，Int.J.Plant Genomics 2008（2008）1-9.

［30］M.Lei，H.H.Li，L.Y.Zhang，J.K.Wang，QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations，Crop J.121（2015）269-283.

［31］D.D.Kosambi，The estimation of map distances from recombination values，Ann.Hum.Genet.12（1943）172-175.

［32］H.H.Li，G.Y.Ye，J.K.Wang，A modified algorithm for the improvement of composite interval mapping，Genetics 175（2007）361-374.

［33］P.Bradbury，Z.Zhang，D.Kroon，T.Y.Casstevens，E.Buckler，TASSEL:software for association mapping of complex traits in diverse samples，Bioinformatics 23（2007）2633-2635.

［34］B.Fethi，Genetic adaptability of inheritance of resistance to biotic and abiotic stress level on crop:role of epistasis，Afr.J. Biotechnol.10（2011）19913-19917.

［35］H.M.Ariyarathne，D.P.Coyne，G.Jung，P.W.Skroch，A.K. Vidaver，J.R.Steadman，P.N.Miklas，M.J.Bassett，Molecular mapping of disease resistance genes for halo blight，common bacterial blight，and bean common mosaic virus in a segregating population of common bean，J.Am.Soc.Hortic. Sci.124（1999）654-662.

［36］G.Perry，C.DiNatale，W.L.Xie，A.Navabi，Y.Reinprecht，W. Crosby，K.F.Yu，C.Shi，K.P.Pauls，A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes，F(xiàn)ront.Plant Sci.2013（2013）389-393.

［37］M.K.Sekhwal，P.C.Li，I.Lam，X.Wang，S.Cloutier，F(xiàn).M.You，Disease resistance gene analogs（RGAs）in plants，Int.J.Mol. Sci.16（2015）19248-19290.

［38］C.J.Harris，E.J.Slootweg，A.Goverse，D.C.Baulcombe，Stepwise artificial evolution of a plant disease resistance gene，Proc.Natl.Acad.Sci.U.S.A.110（2013）21189-21194.

［39］S.M.Cho，S.H.Shin，K.S.Kim，Y.C.Kim，M.Y.Eun，B.H.Cho，Enhanced expression of a gene encoding a nucleoside diphosphate kinase 1（OsNDPK1）in rice plants upon infection with bacterial pathogens，Mol.Cells 18（2004）390-395.

［40］M.D.Lehti-Shiu，C.Zou，K.Hanada，S.H.Shiu，Evolutionary history and stress regulation of plant receptor-like kinase/ pelle genes，Plant Physiol.150（2009）12-26.

［41］S.S.Marla，V.K.Singh，LOX genes in blast fungus（Magnaporthe grisea）resistance in rice，F(xiàn)unct.Integr.Genomics 12（2012）265-275.

［42］J.Xu，X.Y.Wang，W.Z.Guo，The cytochrome P450 superfamily: key players in plant development and defense，J.Integr.Agric. 14（2015）1673-1686.

［43］Y.Y.Song，D.M.Chen，K.Lu，Z.X.Sun，R.S.Zeng，Enhanced tomato disease resistance primed by arbuscular mycorrhizal fungus，F(xiàn)ront.Plant Sci.6（2015）786.

［44］R.M.Givens，M.H.Lin，D.J.Taylor，U.Mechold，J.O.Berry，V.J. Hernandez，Inducible expression，enzymatic activity，and origin of higher plant homologues of bacterial RelA/SpoT stress proteins in Nicotiana tabacum，J.Biol.Chem.279（2004）7495-7504.

［45］A.R.Barman，J.Banerjee，Versatility of germin-like proteins in their sequences，expressions，and functions，F(xiàn)unct.Integr. Genomics 15（2015）1-16.

［46］J.Breen，M.Bellgard，Germin-like proteins（GLPs）in cereal genomes:gene clustering and dynamic roles in plant defence，F(xiàn)unct.Integr.Genomics 10（2010）463-476.

［47］B.C.Collard，D.J.Mackill，Marker-assisted selection:an approach for precision plant breeding in the twenty-first century，Philos.Trans.R.Soc.Lond.B Biol.Sci.363（2008）557-572.

［48］T.Toojinda，S.Tragoonrung，A.Vanavichit，J.L.Siangliw，N. Pa-In，J.Jantaboon，M.Siangliw，S.Fukai，Molecular breeding for rainfed lowland rice in the Mekong region，Plant Prod.Sci. 8（2005）330-333.

［49］G.Abalo，P.Tongoona，J.Derera，R.Edema，A comparative analysis of conventional and marker-assisted selection methods in breeding maize streak virus resistance in maize，Crop Sci.49（2009）509-520.

［50］P.K.Gupta，P.Langridge，R.R.Mir，Marker-assisted wheat breeding:present status and future possibilities，Mol.Breed. 26（2010）145-161.

［51］http://faostat3.fao.org/browse/Q/QC/E

3 May 2016

in revised form

Abbreviations：CBB，common bacterial blight；Xap，Xanthomonas axonopodis pv.phaseoli；Xff，X.fuscans subsp.fuscans；Long 5，Longyundou 5；Long 4，Longyundou 4；DAI，days after inoculation；QTL，quantitative trait loci（locus）；SSR，simple sequence repeat；SCAR，sequence characterized amplified region；MAS，marker-assisted selection；RAPD，random amplified polymorphic DNA；PCR，polymerase chain reaction；ICIM，inclusive composite interval mapping；ICIM-ADD，inclusive composite interval mapping of additive QTL；ICIM-EPI，inclusive composite interval mapping of epistatic QTL；PVE，percentage of variance explained；GLP，germin like protein；NDPK，nucleoside diphosphate kinase；PK，protein kinase；LOX，lipoxygenase；CYP，cytochrome P450；PKc，protein kinase C；OxO，oxalate oxidase；SOD，superoxide dismutase；AGPPase，ADP glucose pyrophosphatase/phosphodiesterase；PPO，polyphenol oxidase；DA，dominant-additive；AD，additive-dominant；DD，dominant-dominant；SNP，single-nucleotide polymorphism.

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E-mail address:wangshumin@caas.cn（S.Wang）.

Peer review under responsibility of Crop Science Society of China and Institute of Crop Science，CAAS.

http://dx.doi.org/10.1016/j.cj.2016.06.009

2214-5141/?2016 Crop Science Society of China and Institute of Crop Science，CAAS.Production and hosting by Elsevier B.V.This is an open access article under the CC BY-NC-ND license（http://creativecommons.org/licenses/by-nc-nd/4.0/）.