Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

Abstract

Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1–C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima’s D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima’s D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.

Deciphering diversity at er loci for diversification of powdery mildew resistance in pea

“…A low value of nd (0.01606) and a negative value of Tajima's D -2.09021 at P < 0.05 (statistically significant) revealed that these resistant lines can’t be affected by environmental conditions. Nucleotide diversty (nd) of the cultivated varieties of Korean rice accessions (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) was found to be lower, revealed no reduction in diversity during domestication 47 . To illustrate the molecular data for intraspecific studies, various haplotype networks were previously used 48 .…”

Analysis and Research on Starch Content and Its Processing, Structure and Quality of 12 Adzuki Bean Varieties

“…Illustratively, the synthesis of sucrose was controlled by sucrose phosphate synthase (SPS), while an enzyme–sucrose synthase (SS) catalyzed the sucrose degradation. Finally, under the action of these starch synthases, the synthetic starch was stored in the grain [ 25 ].…”

OsAT1, an anion transporter, negatively regulates grain size and yield in rice

“…For instance, the expression levels of the granule‐bound starch synthase gene GBSSII, β‐ glucosidase (OsBGLU1) and fructokinase (OsFRK1) decreased in the OsAT1 ‐OE lines seeds (Figure 7C). GBSSII is a grain quality (eating and cooking quality) determinant of amylose content in the seed endosperm (Dian et al, 2003; Maung et al, 2021). These findings are consistent with the differentially expressed genes between OsAT1 ‐OE, OsAT1 ‐Ri, and WT, suggesting that OsAT1 may influence the expression of starch biosynthesis‐related genes.…”