Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine max L.)

Abstract

Key message Two major QTLs associated with low seed coat deficiency of soybean seeds were identified in two biparental populations, and three SNP markers were validated to assist low-SCD natto soybean breeding selection. Abstract Soybean seed coat deficiency (SCD), known as seed coat cracking during soaking in the natto production process, is problematic because split or broken beans clog production lines and increases production costs. Development of natto soybean cultivars with low SCD is crucial to support the growth of the natto industry. Unfortunately, information on the genetic control of SCD in soybean, which is desperately needed to facilitate breeding selection, remains sparse. In this study, two F2 populations derived from V11-0883 × V12-1626 (Pop 1) and V11-0883 × V12-1885 (Pop 2) were developed and genotyped with BARCSoySNP6K Beadchips and F2-derived lines were evaluated for SCD in three consecutive years (2016–2018) in order to identify quantitative trait loci (QTLs) associated with low SCD in soybean. A total of 17 QTLs underlying SCD were identified in two populations. Among these, two major and stable QTLs, qSCD15 on chromosome 15 and qSCD20 on chromosome 20, were detected across multiple years. These QTLs explained up to 30.3% of the phenotypic variation for SCD in Pop 1 and 6.1% in Pop 2 across years. Three SNP markers associated with the qSCD20 were validated in additional four biparental populations. The average selection efficiency of low-SCD soybean was 77% based on two tightly linked markers, Gm20_34626867 and Gm20_34942502, and 64% based on the marker Gm20_35625615. The novel and stable QTLs identified in this study will facilitate elucidation of the genetic mechanism controlling SCD in soybean, and the markers will significantly accelerate breeding for low-SCD soybean through marker-assisted selection.

Mining of seed coat cracking related genetic loci and genes in diverse soybean (Glycine max) populations

“…For example, we detected QTL qSCC‐B1 (3.9–4.4 Mb) on chromosome 11 in E1 environment and BLUP value, which showed a far distance (~4.8 Mb) from the reported QTLs ( qSCC11‐1 and qCS11‐1 ) in previous studies (Ha et al, 2012; Yamaguchi et al, 2015). Meanwhile, the associated SNP ss715620540 for the type‐I SCC on chromosome 15 in our study also had a far distance (~6.8 Mb) with reported QTL qSCD20 in previous study (Zhu et al, 2020).…”

“…with reported QTL qSCD20 in previous study (Zhu et al, 2020). predicted Glyma.20G128600 as a candidate gene for SCC that attributed to the GroES-like zinc-binding alcohol dehydrogenase family and related to the lignin biosynthesis in plants.…”

Development of Breeder-Friendly KASP Markers for Low Concentration of Kunitz Trypsin Inhibitor in Soybean Seeds

“…The SNPs tightly linked to major QTL identified in the mapping population ( Table 7 ) were converted into Kompetitive Allele Specific PCR (KASP) SNP genotyping assays (LGC, Middlesex, UK) with the flanking sequences obtained from the G. max genome Glyma.Wm82.a1 (Schmutz et al 2010) following Zhu et al [ 46 ]. Briefly, the KASP oligos were synthesized by IDT (IDT, Iowa, USA), with primers carrying FAM tail (5′-GAAGGTGACCAAGTTCATGCT-3′) or VIC tail (5′-GAAGGTCGGAGTCAACGGATT-3′), and the target SNP in the 3′ end.…”

“…Briefly, the KASP oligos were synthesized by IDT (IDT, Iowa, USA), with primers carrying FAM tail (5′-GAAGGTGACCAAGTTCATGCT-3′) or VIC tail (5′-GAAGGTCGGAGTCAACGGATT-3′), and the target SNP in the 3′ end. Primer mix and PCR reaction was set up following LGC Genomics recommendation (46 µL distilled water, 30 µL common primer [100 µM], and 12 µL of each tailed primer [100 µM]) [ 46 ]. Thermocycling conditions consisted of the initial hot-start step at 95 °C for 15 min., followed by 10 cycles of touchdown PCR (annealing 65 °C to 57 °C, decreasing 0.8 °C per cycle), then 35 cycles of 20 s at 94 °C and 60 s at 57 °C.…”

“…Thermocycling conditions consisted of the initial hot-start step at 95 °C for 15 min., followed by 10 cycles of touchdown PCR (annealing 65 °C to 57 °C, decreasing 0.8 °C per cycle), then 35 cycles of 20 s at 94 °C and 60 s at 57 °C. PCR and fluorescent endpoint reading were performed in FLUOstar Omega microplate reader (BMG LABTECH) [ 46 ].…”