Genome-wide Association Studies And Candidate Gene Identification For First And Full Flowering Times And Plant Height In Soybean

Soybean,originated from China,is an important economic crop and has important value in food,feeding and industry.Soybean is a very sensitive crop to photoperiod that can affect its flowering time,which seriously limits the planting area of soybean.Furthermore,plant height can affect lodging resistance and yield of soybean.Therefore,the flowering time and plant height in soybean are important objective characters in soybean breeding.To investigate and mine the genes that regulate flowering time and plant height has great significance to improve soybean yield,and also can provide theoretical guidance for soybean molecular breeding.Previous genome-wide association studies(GWAS)for flowering time and plant height in soybean used single-locus methods.Although these methods control the effect of both population structure and polygenic background,they are involved in multiple testing.This kind of testing induced lower significant level of each test and made it difficult to detect the significant association loci,especially under the situation of large errors in field experiments.In addition,the number of molecular markers was relatively small in the GWAS for the above two traits.Therefore,286 soybean accessions were selected as experimental materials from six different ecological areas in China;all the accessions were phenotyped for the first flowering and full flowering times in Nanjing(2011 and 2012),Ezhou(2017)and Wuhan(2017),and for plant height in Wuhan(2014,2015 and 2017)and Ezhou(2017);all the accessions were genotyped by 106013 SNP markers,which were uniformly distributed on the entire genome.Using six multi-locus GWAS methods(mrMLM,FASTmrMLM,FSATmrEMMA,pLARmEB,pKWmEB,and ISIS EM-BLASSO)in the software mrMLM,first,all the SNPs markers were used to be associated with the above three traits.Around the significantly associated QTNs,then,bioinformatics methods were used to mine their candidate genes.Using the common QTNs across various methods or environments(years / locations),finally,elite alleles were mined and molecular breeding was designed.The main results are as follows:1.The results from analysis of variance showed that very significant genetic differences existed among accessions and across environments(years/locations)for the first and full flowering times,and among accessions,across enviroments,and accession-by-environment interaction for plant height.The generalized heritabilities for the first and full flowering times and plant height were 82.43,80.27 and 76.55(%),respectively.In 2017,the correlation coefficients between plant height and the first and full flowering times were 0.556 and 0.550 in Ezhou,and 0.556 and 0.550 in Wuhan,respectively.This indicates a significant positive correlation at the 0.01 level between flowering time and plant height at the same environment.2.Six multi-locus genome-wide addosition study methods(FASTmrMLM,mrMLM,FSATmrEMMA,pLARmEB,pKWmEB and ISIS EM-BLASSO)were used to associate the 106013 SNP markers of 286 soybean accessions with the above three traits.At the critical LOD score of 3.0 for significantly associated QTNs,a total of 185,161 and 129 SNPs were found to be associated with the first and full flowering times and plant height,respectively.Among the above 475 QTNs,60,57 and 43 were repeatedly detected at least two methods or two environments for the above three traits,respectively.3.Within 50 kb of QTNs repeatedly detected for the first and full flowering times and plant height,445,461 and 339 genes were found,respectively.Among these genes,121,119 and 88 for the above three traits were highly expressed in flowers and stems,respectively.These highly expressed genes were used to conduct KEGG analysis.As a result,7,9 and 8 genes for the three traits were found to be related to their corresponding metabolic pathways.These genes were compared with their homologous genes in Arabidopsis,we found that twelve candidate genes were related to flowering time,and eight candidate genes were related to plant height.4.The average numbers of elite alleles in each of 286 soybean accessions for the first and full flowering times were 31.78(11 to 48)and 32.30(14 to 48),respectively.The average number of elite alleles in each of 272 soybean accessions(no wild soybeans)for plant height was 17.75(7 to 36).The correlation coefficients between the number of elite alleles and phenotypic observations for the above three traits were-0.791,-0.749 and 0.630(P<0.0001),respectively,indicating negative correlation between the number of elite alleles and flowering time and positive correlation between the number of elite alleles and plant height.Through the above analyses,Fengshouhuangdou,Niumaohuang,Shangqiu 73,Jindou 3,Pingyuanxianheidou,Qinyan 1 and Caishengzi might be used as excellent parents to improve flowering time;Yanqing,Zunyizongzidou,Shuichengzongzidou,Yongshenghupihuangdou,Puchengmadou,Dalihuangdou,Xilibayuebao and Beichuanwuyanwo might be used as excellent parents to improve plant height.If the first flowering time was improved,the Shangqiu 73 and Fengshouhuangdou cross is available,because their progeny might have 55 elite alleles,which produce the shortest first flowering time in theory.If the full flowering time was improved,the Pingyuanxianheidou × Jindou 3 and Qindou 1 × Caishengzi crosses are available,because their progeny might have 52 elite alleles,which produce the shortest full flowering time in theory.If plant height was improved,the Yanqing × Zunyizongzidou,Yanqing × Shuichengzongzidou,Yongshenghupihuangdou × Puchengmadou,Yongshenghu pihuangdou × Dalihuangdou,Xilibayuebao × Beichuanwuyanwo crosses were available,because their progeny might have 24,24,23,24 and 25 elite alleles,respectively,which produce semi-dwarf plant(70 ~ 80 cM)in theory.