Construction Of SNP High-density Genetic Map And QTL Analysis Of Agronomic Traits In Cowpea(Vigna Unguiculata(L.) Walp.)

Genetic map is helpful to explore molecular markers linked to important traits,providing information for constrcuting marker assisted breeding technology platform,and promoting the breeding process of new varieties.Previous cowpea genetic maps are in low density,leading to less efficiency for new gene mining and location.We hereby constructed a cowpea SNP map based on the genotypic and phenotypic data of F_2-3population derived from common cowpea and yard long bean in this study,and performed the QTL mapping and candidate gene screening for several important traits.The main results are as follows:1.The average depth of genome coverage for both parents was more than 20X,and the average depth of offspring coverage was 3.19x.The Q30 of male parent,female parent and progeny were 93.45%,92.48%,93.22%,respectively,and GC content was36.04%,36.08%,35.72%,respectively.A total of 1,070,323 SNPS were detected between parents,where the conversion variation accounted for 68.4%and transmutation accounted for 31.6%.There were 941,285 homozygous SNPS detected in the mother line,accounting for 87.94%,and 999,315 homozygous SNPS detected in the father line,accounting for 93.37%.After screening and filtering,a total of 146,697 high-quality SNPS were obtained,dividing into 3061 Bin markers according to 15 step sizes.Finally,a total of 2984 Bin（142,146 SNP）were mapped to 11 linkage groups using Highmap,with a total genetic distance of 1333.48 c M and an average map distance of 0.45c M.The length of linkage group was LG10（183.15 c M）>LG3（137.76 c M）>LG9（136.10 c M）>LG5（130.46 c M）>LG4（129.47 c M）>LG11（121.57 c M）>LG8（111.80 c M）.>LG6（103.91 c M）>LG7（100.75 c M）>LG1（93.68 c M）>LG2（84.63 c M）.The average genetic distance of linkage group was LG4（0.89 c M）>LG10（0.63 c M）>LG6（0.54 c M）>LG7（0.52 c M）>LG1（0.51 c M）>LG5（0.47 c M）>LG9（0.46 c M）>LG2（0.45）CM)>LG8（0.39 c M）>LG11（0.29 c M）>LG3（0.27 c M）.There were 4 gaps on the map larger than 5c M,distributing in linkage group LG3,LG4,LG6 and LG10.2.A total of 19 QTL loci were detected for 14 traits in F₂ and F₃ populations.The F₂population of the communist party of China to detect 13 QTL,pod is qualitative,main stem branching number,grain density and mature period four properties such as QTL were not detected,pod length,grain composition,color design and color,navel ring color,kind of,the number of pods per plant,though single pod grain number,pod and hundred grain weight,pod 10 properties such as color were detected in 13 QTL loci,These QTL loci were distributed in 12 regions,and the distribution of the mapping regions on the linkage group（chromosome）was LG3（1）,LG5（2）,LG7（4）,LG8（2）,LG9（2）,and LG11（1）.In F₃ families,a total of 16 QTL loci were detected for 14 traits,and these QTL loci were distributed in 12 intervals,which were distributed in linkage groups（chromosomes）:LG1（1）,LG3（1）,LG5（1）,LG7（4）,LG8（2）,LG9（2）,and LG11（1）.The QTL mapping results of F₂ and F₃ families showed that the mapping results of seven traits,including100-grain weight,pod color,flower color,type of seed color,presence or absence of hilum color,number of pods per plant and pod number per plant,were consistent in different generations.Two QTLS for pod length and seed coat color were detected in F₂generation,but only one QTL was detected in F₃ family.Two QTLS were detected in F₃ family and only one QTL was detected in F₂ population.In addition,QTLS for pod quality,maturity,grain density and main stem branch number were only detected in F₃ families.3.A total of 62 non-synonymous mutations were found in the above 19 QTL intervals.Further analysis revealed that the non-synonymous mutation LOC114178564in the QTL segment of Chr3 was related to mitogen-related microtubulin regulation and might be a candidate gene for pod length related,and the non-synonymous mutation LOC114196343 located at Chr9 was described as protein transparent seed coat.While LOC114193834 and LOC114193715,two non-synonymous mutations at Chr8,are both related to cellulose synthase-like proteins,and might be related to the regulation of pod number per plant.