First pod height (FPH) of soybeans is an important trait for reducing seed loss occurred by a combine harvester. To identify genetic regions associated with FPH, 387 soybean germplasm was used for GWAS and two F 6:7 recombinant inbred line (RIL) populations comprising 167 lines from Uram × Chamol cr...
First pod height (FPH) of soybeans is an important trait for reducing seed loss occurred by a combine harvester. To identify genetic regions associated with FPH, 387 soybean germplasm was used for GWAS and two F 6:7 recombinant inbred line (RIL) populations comprising 167 lines from Uram × Chamol cross, and 174 lines from Uram × Milyang257 cross were used for QTL analysis. Phenotype evaluation was conducted in the Daegu experiment station (Rep. of Korea) for 2 years (2016 and 2017). Germplasm for GWAS and RILs were genotyped with 50K SNP and 180K SNP, respectively. The result of GWAS, ss715623618 in chromosome 16 (C2) showed a significance (p<0.00001) for FPH. SNP variation (adenosine/guanine) also showed FPH variations. Glyma.16g107300 was located near the identified region and related to function of cell wall synthesis. Glyma.16g106800 was located near ss715623623 in the LD block and related to xylan synthesis and leucine-rich repeat (LRR) receptor-like protein kinase. In the QTL analysis, 12 QTLs for FPH were identified. The QTLs, qFPH10_1A and qFPH10_1B, localized on chromosome 10 were consistently detected, and hence were further characterized for identifying candidate genes. In this region, 5 out of 60 genes were showed SNP variation in re-sequencing of parental lines. The sequence comparison between the parental lines revealed 10 SNPs on candidate genes, and sequence deletion was detected on Glyma.10g228100 for lower-FPH parent ‘Chamol’. The functions of candidate genes, Glyma.10g221500, Glyma.10g221700, Glyma.10g221800, Glyma.10g227700, and Glyma.10g228100, were regulation of circadian rhythm, membrane constituent, biological process, glycosyl hydrolase family 18, and LRR protein for BR1 (brassinosteroid signal transmission), respectively. Genotyping of RILs revealed that higher FPH was co-segregated with the genotypes of ‘Uram’. In the result of multi-environment trial analysis, FPH was comparably high variable, and showed third variable trait out of 10 traits with CV 33.1%. Stability index and GGEBiplot showed that higher stability and performance genotypes were M307 and M327 in 2017, M306 in 2018, M344 and M361 in 2019, and M376 and M361 in 2020, respectively. Environment focused AEC in GGEBiplot indicated Yeasan was better environment for FPH evaluation. Which-one-where polygon view showed that Iksan, Naju, Jinju, Yeoncheon could be mega-environment in specific year. The result of this study can provide the background information of environmental and genetic effect for FPH to soybean breeders and scientists.
First pod height (FPH) of soybeans is an important trait for reducing seed loss occurred by a combine harvester. To identify genetic regions associated with FPH, 387 soybean germplasm was used for GWAS and two F 6:7 recombinant inbred line (RIL) populations comprising 167 lines from Uram × Chamol cross, and 174 lines from Uram × Milyang257 cross were used for QTL analysis. Phenotype evaluation was conducted in the Daegu experiment station (Rep. of Korea) for 2 years (2016 and 2017). Germplasm for GWAS and RILs were genotyped with 50K SNP and 180K SNP, respectively. The result of GWAS, ss715623618 in chromosome 16 (C2) showed a significance (p<0.00001) for FPH. SNP variation (adenosine/guanine) also showed FPH variations. Glyma.16g107300 was located near the identified region and related to function of cell wall synthesis. Glyma.16g106800 was located near ss715623623 in the LD block and related to xylan synthesis and leucine-rich repeat (LRR) receptor-like protein kinase. In the QTL analysis, 12 QTLs for FPH were identified. The QTLs, qFPH10_1A and qFPH10_1B, localized on chromosome 10 were consistently detected, and hence were further characterized for identifying candidate genes. In this region, 5 out of 60 genes were showed SNP variation in re-sequencing of parental lines. The sequence comparison between the parental lines revealed 10 SNPs on candidate genes, and sequence deletion was detected on Glyma.10g228100 for lower-FPH parent ‘Chamol’. The functions of candidate genes, Glyma.10g221500, Glyma.10g221700, Glyma.10g221800, Glyma.10g227700, and Glyma.10g228100, were regulation of circadian rhythm, membrane constituent, biological process, glycosyl hydrolase family 18, and LRR protein for BR1 (brassinosteroid signal transmission), respectively. Genotyping of RILs revealed that higher FPH was co-segregated with the genotypes of ‘Uram’. In the result of multi-environment trial analysis, FPH was comparably high variable, and showed third variable trait out of 10 traits with CV 33.1%. Stability index and GGEBiplot showed that higher stability and performance genotypes were M307 and M327 in 2017, M306 in 2018, M344 and M361 in 2019, and M376 and M361 in 2020, respectively. Environment focused AEC in GGEBiplot indicated Yeasan was better environment for FPH evaluation. Which-one-where polygon view showed that Iksan, Naju, Jinju, Yeoncheon could be mega-environment in specific year. The result of this study can provide the background information of environmental and genetic effect for FPH to soybean breeders and scientists.
주제어
#콩 착협고 GWAS QTL Stability
※ AI-Helper는 부적절한 답변을 할 수 있습니다.