Genetics and mapping of seed coat impermeability in soybean using inter-specific populations

Abstract

Seed coat impermeability (SCI) in soybean is associated with seed viability under storage and quality of processed products. Understanding genetics and identification of linked molecular markers would facilitate need-based utilization of seed coat impermeability. Two impermeable wild type (G. soja Sieb. and Zucc.) accessions viz. PI 424079 and PI 136620 were crossed with a permeable cultivated (G. max) variety JS335 to generate the mapping populations. Genetic analysis of the F 1:2 and F 2:3 seeds of the crosses indicated that SCI is controlled by a single gene/major QTL, and impermeability is dominant over permeability. Presence of seeds with intermediate permeability indicated role of some minor genes/QTLs. A set of 204 inter-specific recombinant inbred line (RILs) (F 7 ) was used to map SCI with 207 SSR markers. Phenotyping through rapid imbibition approach (seed imbibition for 6 h), seven QTLs were mapped on chromosomes (Chrs.) 2, 5, 12, 13 and 16 in the seeds stored for 1-3 years, while through slow imbibition method (seed imbibition for 7 days), five QTLs were mapped on Chrs. 2, 9, 10 and 20. Phenotypic variation explained (PVE) by the QTLs ranged from 5.96 to 39.67%. Two major and stable QTLs viz., qScI-h2-1 and qScI-h2-2 that mapped in tandem on Chr.2 jointly explained 43.09-62.92% of the variations in impermeability. Seven minor QTLs identified here were novel and two (qScI-h5, and qScI-h16) were consistent. It is the first report of mapping impermeability using two imbibition approaches together in 200 plus interspecific RILs in soybean. The study will pave the way for developing genotypes with restricted permeability, enhanced seed viability, and improved seeds quality.

Seed longevity studies in wild type, cultivated and inter-specific recombinant inbred lines (RILs) of soybean [Glycine max (L.) Merr.]

“…Causes of such discrepancies include variation in tested genotypes, populations used, approached followed, criteria adopted, etc. (Chandra et al 2020) The studies reported earlier have had used seeds stored for one or two years only. Further, no reports could be found where wild type soybeans viz.…”

Research advances on the hard seededness trait of soybean and the underlying regulatory mechanisms

“…A point mutation (G to T at the 863 rd site of its coding sequence) introduced an amino acid substitution (Ser to Iso at the 288 th site of its protein sequence) in a substrate-binding cleft of the enzyme, possibly reducing or eliminating its affinity for substrates in permeable cultivars from various regions, while the allele from the HS genotype was found to promote the accumulation of b-1,4-glucan derivatives that reinforce the HS trait (Jang et al, 2015). The above two genes are both located within the previously reported chromosome 2 interval and are adjacent in position (Sakamoto et al, 2004;Liu et al, 2007;Kebede et al, 2014;Chen et al, 2019;Chandra et al, 2020) and may be related to the strength of the palisade layer of the seed coat. Wang et al (2022) found that a polygalacturonase gene PG031 (Glyma.06G207300) was specifically expressed in the flowers and reproductive tissues of soybean plants, and that it was strongly induced when the seed coat absorbs water.…”

“…Based on bulked segregant analysis and traditional linkage mapping, three HS QTLs were detected on chromosomes 2, 3, and 6, respectively, which explained 4.9%-23.3% of the phenotypic variation. Chandra et al (2020) constructed 204 RILs by crossing two wild soybean accessions with a permeable soybean cultivar, and seven HS QTLs were mapped on chromosomes 2, 5, 12, 13, and 16, respectively, explaining 5.96%-39.67% of the phenotypic variations. Two main and stable QTLs distributed in tandem on chromosome 2 were consistent over the 3 years of testing, and they jointly explained 43.09%-62.92% of the phenotypic variations of the HS trait.…”

Research Advances on the Hard Seededness Trait of Soybean and the Underlying Regulatory Mechanisms

“…A point mutation (G to T at the 863rd site of its coding sequence) introduced an amino acid substitution (Ser to Iso at the 288th site of its protein sequence) in a substrate-binding cleft of the enzyme, possibly reducing or eliminating its affinity for substrates in permeable cultivars from various regions, while the allele from the HS genotype was found to promote the accumulation of β-1,4-glucan derivatives that reinforce the HS trait [86]. The above two genes are both located within the previously reported chromosome 2 interval and are adjacent in position and may be related to the strength of the palisade layer of the seed coat [5,40,41,84,85]. Wang et al, [87] found that a polygalacturonase gene PG031 (Glyma.06G207300) was specifically expressed in the flowers and reproductive tissues of soybean plants, and that it was strongly induced when the seed coat absorbs water.…”

“…Based on bulked segregant analysis and traditional linkage mapping, three HS QTLs were detected on chromosomes 2, 3, and 6, respectively, which explained 4.9%-23.3% of the phenotypic variation. Chandra et al, [85] constructed 204 RILs by crossing two wild soybean accessions with a permeable soybean cultivar, and seven HS QTLs were mapped on chromosomes 2, 5, 12, 13, and 16, respectively, explaining 5.96%-39.67% of the phenotypic variations. Two main and stable QTLs distributed in tandem on chromosome 2 were consistent over the 3 years of testing, and they jointly explained 43.09%-62.92% of the phenotypic variations of the HS trait.…”