Population structure and association mapping studies for important agronomic traits in soybean

Abstract

The present study was carried out with a set of 96 diverse soybean genotypes with the objectives of analysing the population structure and to identify molecular markers associated with important agronomic traits. Large phenotypic variability was observed for the agronomic traits under study indicating suitability of the genotypes for association studies. The maximum values for plant height, pods per plant, seeds per pod, 100-seed weight and seed yield per plant were approximately two and half to three times more than the minimum values for the genotypes. Seed yield per plant was found to be significantly correlated with pods per plant (r = 0.77), 100-seed weight (r = 0.35) and days to maturity (r = 0.23). The population structure studies depicted the presence of seven subpopulations which nearly corresponded with the source of geographical origin of the genotypes. Linkage disequilibrium (LD) between the linked markers decreased with the increased distance, and a substantial drop in LD decay values was observed between 30 and 35 cM. Genomewide marker-traits association analysis carried out using general linear (GLM) and mixed linear models (MLM) identified six genomic regions (two of them were common in both) on chromosomes 6, 7, 8, 13, 15 and 17, which were found to be significantly associated with various important traits viz., plant height, pods per plant, 100-seed weight, plant growth habit, average number of seeds per pod, days to 50% flowering and days to maturity. The phenotypic variation explained by these loci ranged from 6.09 to 13.18% and 4.25 to 9.01% in the GLM and MLM studies, respectively. In conclusion, association mapping (AM) in soybean could be a viable alternative to conventional QTL mapping approach.

Photosynthesis in a Changing Global Climate: Scaling Up and Scaling Down in Crops

“…Indeed, putative QTLs have been detected for Single-Photon Avalanche Diode (SPAD) value, chlorophyll content, stomatal conductance, sink size, source strength, carbon isotope discrimination, and carbohydrate translocation ( Ulloa et al, 2000 ; Teng et al, 2004 ; Takai et al, 2010 , 2013 ). Potential QTLs have been revealed also for net CO 2 assimilation rate (A n ) in rice ( Ishimaru et al, 2001 ; Price et al, 2002 ; Zhao et al, 2011 ; Hirotsu et al, 2017 ; Ye et al, 2017 ; Adachi et al, 2019 ), barley ( Teulat et al, 2002 ; Cantalapiedra et al, 2015 ; Liu et al, 2017 ; Du et al, 2019 ), maize ( Fracheboud et al, 2002 ), soybean ( Jun et al, 2014 ; Lv et al, 2018 ; Liu D. et al, 2019 ), cucumber ( Zhang et al, 2004 ), and legumes ( Muchero et al, 2009 ; Kumar et al, 2014 ; Li F. et al, 2015 ). In the case of rice, several loci enhancing leaf A n have been detected on chromosomes 3, 4, 5, 6, 8, 9, and 11 ( Adachi et al, 2011 ; Gu et al, 2012 ).…”

Analysis of spatial distribution of genetic diversity and validation of Indian foxtail millet core collection

“…Pritchard et al (2000) suggested that population structure is difficult to detect using visible traits however; it may be easily detectable with molecular characters. Recently, population structure has been studied by many researchers in foxtail millet (Gupta et al 2014;Vetriventhan et al 2014;Ali et al 2016), broomcorn millet (Liu et al 2016), finger millet (Ramakrishnan et al 2016), sorghum (Kondombo et al 2016), Solanum pimpinellifolium (Rao et al 2012) and soybean (Kumar et al 2014).…”

Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea

“…Considering the added-advantages of QTL and association mapping in quantitative dissection of complex traits, a number of genes underlying QTLs associated with plant height that rely on these approaches, have been identified in crop plants, including legumes39404142434445464748495051525354. Similar major efforts have been made in the past few years towards molecular mapping of low-resolution QTLs governing plant height on multiple intra- as well as inter-specific genetic linkage maps of chickpea629343755565758.…”