Mapping and validation of simple sequence repeat markers linked to a major gene controlling seed cadmium accumulation in soybean [Glycine max (L.) Merr]

Abstract

Daily consumption of cadmium (Cd) contaminated foods poses a risk to human health. Cultivar selection is an important method to limit Cd uptake and accumulation; however, analyzing grain Cd concentration is costly and time-consuming. Developing markers for low Cd accumulation will facilitate marker assisted selection (MAS). Inheritance studies using a threshold value of 0.2 mg kg(-1) for low and high and an F(2:3) population showed that low Cd accumulation in soybean seed is under the control of a major gene (Cda1, proposed name) with the allele for low accumulation being dominant. A recombinant inbred line (RIL) population (F(6:8)) derived from the cross AC Hime (high Cd accumulation) and Westag-97 (low Cd accumulation) was used to identify the DNA markers linked to Cda gene(s) or quantitative trait loci (QTLs) controlling low Cd accumulation. We screened 171 simple sequence repeat (SSR) primers that showed polymorphism between parents on the 166 RILs. Of these, 40 primers were newly developed from the soybean genomic DNA sequence. Seven SSR markers, SatK138, SatK139, SatK140 (0.5 cM), SatK147, SacK149, SaatK150 and SattK152 (0.3 cM), were linked to Cda1 in soybean seed. All the linked markers were mapped to the same linkage group (LG) K. The closest flanking SSR markers linked to Cda1 were validated using a parallel population (RILs) involving Leo x Westag-97. Linked markers were also validated with diverse soybean genotypes differing in their seed Cd concentration and showed that SSR markers SatK147, SacK149, and SattK152 clearly differentiated the high and low Cd accumulating genotypes tested. To treat Cd uptake as a quantitative trait, QTL analysis using a linkage map constructed with 161 markers identified a major QTL associated with low Cd concentration in the seeds. The QTL was also mapped to the same location as Cda1 on LG-K. This QTL accounted for 57.3% of the phenotypic variation. Potential candidate genes (genes with known or predicted function that could influence the seed Cd concentration) like protein kinase, putative Adagio-like protein, and plasma membrane H(+)-ATPase were found to be located in the locus of interest. Of the four SSR markers located in the region, SattK152 was localized in the plasma membrane H(+)-ATPase gene. SSR markers closely linked to Cda1 in seeds of soybean were identified and have potential to be used for MAS to develop low Cd accumulating cultivars in a breeding program.

Identification of new QTLs for seed mineral, cysteine, and methionine concentrations in soybean [Glycine max (L.) Merr.]

“…Studies on understanding genes and processes to improve seed nutritional composition by identifying quantitative trait loci (QTLs) were limited to a few minerals or nutrients in soybean (Jegadeesan et al 2010;King et al 2013;Panthee et al 2006a;Zhang et al 2009). Four QTLs for seed Ca concentration were detected, one of which accounted for up to 16.3% of variation (Zhang et al 2009).…”

“…Four QTLs for seed Ca concentration were detected, one of which accounted for up to 16.3% of variation (Zhang et al 2009). A major QTL accounted for 57.3% of variation for low cadmium (Cd) in soybean (Jegadeesan et al 2010). A major QTL for seed Fe concentration explained 21.5% of the phenotypic variation (King et al 2013).…”

Comparison of Population Genetic Structures between Asian and American Mungbean Accessions Using SSR Markers

“…DNA-based molecular markers provide powerful tools in studying genetic diversity and population structure techniques for analyzing molecular markers such as restriction fragment length polymorphism (RFLP) (Schutte et al, 2008), random amplification of polymorphic DNA (RAPD) (Dikshit et al, 2007;Lu et al, 2009) amplified fragment length polymorphism (AFLP) (Tatikonda et al, 2009) simple sequence repeats (SSRs) (Chapuis & Estoup, 2007;Lung'aho et al, 2011), and single nucleotide polymorphisms (SNPs) (Ganal, Altmann, & Röder, 2009) are now available. SSRs or microsatellite markers, due to their codominance and high polymorphism, are particularly attractive for studying genetic structure and the relationships between species (Jegadeesan et al, 2010;Lu et al, 2009;Saxena, Saxena, Kumar, Hoisington, & Varshney, 2010;Zhang, Blair, & Wang, 2008). In the present study, genetic structure and diversity of 65 mungbean varieties collected from East and Southeast Asia, the United States and Guatemala were evaluated using 15 SSR markers.…”

Variable dynamics of cadmium uptake and allocation in four soybean cultivars

“…The simple sequence repeat (SSR) genetic markers amplifying the Cda1 locus for low Cd accumulation capacity (Jegadeesan et al 2010) were used. DNA was isolated according to Békésiová et al (1999).…”

“…The workable strategies to address Cd toxicity in plants include selection of genotypes that either demonstrate low uptake or are hyperaccumulators (Jha and Bohra 2016). For several crop species including rice, wheat and soybean have already been identified genetic markers that allow for selection of genotypes with low genetic potential to accumulate cadmium (Jegadeesan et al 2010). In addition to many transporters and channels on the plasma membrane (Van Kerkhove et al 2010), the metal uptake largely depends on the composition and properties of cell walls since they affect metal binding (immobilizing) and filtering capacity, restricting metal entrance to the cells (Parrotta et al 2015).…”