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

Insights into mechanisms of seed longevity in soybean: a review

Soybean, a crop of international importance, is challenged with the problem of seed longevity mainly due to its genetic composition and associated environmental cues. Soybean's fragile seed coat coupled with poor DNA integrity, ribosomal dysfunction, lipid peroxidation and poor antioxidant system constitute the rationale for fast deterioration. Variability among the genotypes for sensitivity to field weathering contributed to their differential seed longevity. Proportion and density of seed coat, glassy state of cells, calcium and lignin content, pore number, space between seed coat and cotyledon are some seed related traits that are strongly correlated to longevity. Further, efficient antioxidant system, surplus protective proteins, effective nucleotide and protein repair systems and free radical scavenging mechanisms also contributed to the storage potential of soybean seeds. Identification of molecular markers and QTLs associated with these mechanisms will pave way for enhanced selection efficiency for seed longevity in soybean breeding programs. This review reflects on the morphological, biochemical and molecular bases of seed longevity along with pointers on harvest, processing and storage strategies for extending vigour and viability in soybean.

Integrated analysis of biparental and natural populations reveals CRIB domain-containing protein underlying seed coat crack trait in watermelon

The scc locus of the watermelon seed coat crack trait was fine mapped on chromosome 3. Cla97C03G056110 (annotated as CRIB domain-containing protein) was regarded as the most likely candidate gene Seed coat crack (scc) is a special characteristic of watermelon compared with other cucurbit crops. However, information regarding the genetic basis of this trait is limited. We conducted a genetic analysis of six generations derived from PI 192938 (scc) and Cream of Saskatchewan (COS) (non-scc) parental lines and found that the scc trait was regulated by a single recessive gene through two years. Bulk segregant analysis sequencing (BSA-seq) and initial mapping placed the scc locus into an 808.8 kb region on chromosome 3. Evaluation of another 1152 F₂ plants narrowed the scc locus to a 277.11 kb region containing 37 candidate genes. Due to the lack of molecular markers in the fine-mapping interval, we extracted the genome sequence variations in this 277.11 kb region with in silico BSA among seventeen re-sequenced lines (6 scc and 11 non-scc) and finally delimited the scc locus to an 8.34 kb region with only one candidate gene Cla97C03G056110 (CRIB domain-containing protein). Three single nucleotide polymorphism loci in the promoter region of Cla97C03G056110 altered cis-acting elements that were highly correlated with the nature watermelon panel. The expression of Cla97C03G056110 in seed coat tissue was higher in non-scc than in scc lines and was specifically expressed in seed coat compared with fruit flesh.

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

Trypsin inhibitors (TI), a common anti-nutritional factor in soybean, prevent animals' protein digestibility reducing animal growth performance. No commercial soybean cultivars with low or null concentration of TI are available. The availability of a high throughput genotyping assay will be beneficial to incorporate the low TI trait into elite breeding lines. The aim of this study is to develop and validate a breeder friendly Kompetitive Allele Specific PCR (KASP) assay linked to low Kunitz trypsin inhibitor (KTI) in soybean seeds. A total of 200 F3:5 lines derived from PI 547656 (low KTI) X Glenn (normal KTI) were genotyped using the BARCSoySNP6K_v2 Beadchip. F3:4 and F3:5 lines were grown in Blacksburg and Orange, Virginia in three years, respectively, and were measured for KTI content using a quantitative HPLC method. We identified three SNP markers tightly linked to the major QTL associated to low KTI in the mapping population. Based on these SNPs, we developed and validated the KASP assays in a set of 93 diverse germplasm accessions. The marker Gm08_44814503 has 86% selection efficiency for the accessions with low KTI and could be used in marker assisted breeding to facilitate the incorporation of low KTI content in soybean seeds.