scholarly journals Identification of QTNs Controlling 100-Seed Weight in Soybean Using Multilocus Genome-Wide Association Studies

2020 ◽  
Vol 11 ◽  
Author(s):  
Zhongying Qi ◽  
Jie Song ◽  
Kaixin Zhang ◽  
Shulin Liu ◽  
Xiaocui Tian ◽  
...  
Keyword(s):  
Seed Weight ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
100 Seed Weight

scholarly journals Identification of QTNs and Their Candidate Genes for 100-Seed Weight in Soybean (Glycine max L.) Using Multi-Locus Genome-Wide Association Studies

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 714 ◽  
Author(s):  
Muhammad Ikram ◽  
Xu Han ◽  
Jian-Fang Zuo ◽  
Jian Song ◽  
Chun-Yu Han ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Marker Assisted Selection ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Single Locus ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
100 Seed Weight

100-seed weight (100-SW) in soybeans is a yield component trait and controlled by multiple genes with different effects, but limited information is available for its quantitative trait nucleotides (QTNs) and candidate genes. To better understand the genetic architecture underlying the trait and improve the precision of marker-assisted selection, a total of 43,834 single nucleotide polymorphisms (SNPs) in 250 soybean accessions were used to identify significant QTNs for 100-SW in four environments and their BLUP values using six multi-locus and one single-locus genome-wide association study methods. As a result, a total of 218 significant QTNs were detected using multi-locus methods, whereas eight QTNs were identified by a single-locus method. Among 43 QTNs or QTN clusters identified repeatedly across various environments and/or approaches, all of them exhibited significant trait differences between their corresponding alleles, 33 were found in the genomic region of previously reported QTLs, 10 were identified as new QTNs, and three (qHSW-4-1, qcHSW-7-3, and qcHSW-10-4) were detected in all the four environments. The number of seed weight (SW) increasing alleles for each accession ranged from 8 (18.6%) to 36 (83.72%), and three accessions (Yixingwuhuangdou, Nannong 95C-5, and Yafanzaodou) had more than 35 SW increasing alleles. Among 36 homologous seed-weight genes in Arabidopsis underlying the above 43 stable QTNs, more importantly, Glyma05g34120, GmCRY1, and GmCPK11 had known seed-size/weight-related genes in soybean, and Glyma07g07850, Glyma10g03440, and Glyma10g36070 were candidate genes identified in this study. These results provide useful information for genetic foundation, marker-assisted selection, genomic prediction, and functional genomics of 100-SW.

scholarly journals Genome-wide association studies of plant architecture-related traits and 100-seed weight in soybean landraces

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoli Zhang ◽  
Wentao Ding ◽  
Dong Xue ◽  
Xiangnan Li ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Weight ◽  
Plant Architecture ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Potential Candidate ◽  
Genome Wide ◽  
100 Seed Weight

Abstract Background Plant architecture-related traits (e.g., plant height (PH), number of nodes on main stem (NN), branch number (BN) and stem diameter (DI)) and 100-seed weight (100-SW) are important agronomic traits and are closely related to soybean yield. However, the genetic basis and breeding potential of these important agronomic traits remain largely ambiguous in soybean (Glycine max (L.) Merr.). Results In this study, we collected 133 soybean landraces from China, phenotyped them in two years at two locations for the above five traits and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). As a result, we found that a total of 59 SNPs were repeatedly detected in at least two environments. There were 12, 12, 4, 4 and 27 SNPs associated with PH, NN, BN, DI and 100-SW, respectively. Among these markers, seven SNPs (AX-90380587, AX-90406013, AX-90387160, AX-90317160, AX-90449770, AX-90460927 and AX-90520043) were large-effect markers for PH, NN, BN, DI and 100-SW, and 15 potential candidate genes were predicted to be in linkage disequilibrium (LD) decay distance or LD block. In addition, real-time quantitative PCR (qRT-PCR) analysis was performed on four 100-SW potential candidate genes, three of them showed significantly different expression levels between the extreme materials at the seed development stage. Therefore, Glyma.05 g127900, Glyma.05 g128000 and Glyma.05 g129000 were considered as candidate genes with 100-SW in soybean. Conclusions These findings shed light on the genetic basis of plant architecture-related traits and 100-SW in soybean, and candidate genes could be used for further positional cloning.

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