Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice

Abstract

Starch is a major ingredient in rice, and the amylose content of starch significantly impacts rice quality. OsSS (starch synthase) is a gene family related to the synthesis of amylose and amylopectin, and 10 members have been reported. In the present study, a synteny analysis of a novel family member belonging to the OsSSIV subfamily that contained a starch synthase catalytic domain showed that three segmental duplications and multiple duplications were identified in rice and other species. Expression data showed that the OsSS gene family is involved in diverse expression patterns. The prediction of miRNA targets suggested that OsSS are possibly widely regulated by miRNA functions, with miR156s targeted to OsSSII-3, especially. Haplotype analysis exhibited the relationship between amylose content and diverse genotypes. These results give new insight and a theoretical basis for the improved amylose content and eating quality of rice.

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

“…Similar to C_3, M_3 exhibited nonsynonymous SNPs. These findings in our study were consistent with the previous findings from a GBSSII haplotype analysis that found that Hap_4 and Hap_5 were the predominant haplotypes of GBSSII haplotyping and the respective rice accessions were mostly from two major rice groups (indica in Hap_4 and japonica in Hap_5) compared to other groups, aus and admixture [20]. Simultaneously, that research group identified a key GBSSII SNP (T/G), which produces significant variations in amylose content.…”

“…Genetic variations (alleles) in crop species, such as SNPs, InDels, and intron length polymorphisms (ILPs), are essential to revealing molecular mechanisms, as they function in controlling traits [47][48][49][50]. Genetic variations of the starch synthase gene family has recently been updated in rice giving new insights into their correlation with improved amylose content and eating quality [20]. Using these identified variations, genetic markers have been developed for various analyses, including genetic diversity assessment, trait association mapping, and fine mapping of QTLs that regulate important agronomic traits [51].…”

“…Haplotype analysis of a specific gene reveals its distinct major dormant and nondormant haplotypes [52] and can also identify many functional alleles which are significantly associated with desired plant traits required for a breeding program, such as eating quality or salt tolerance and resistance [53]. Genome-wide haplotype analysis of the starch synthase gene family recently conducted in rice resulting in the identification of six haplotypes with 17 SNPs were identified in the diverse regions of GBSSII [20]. In our study, a total of 38 functional haplotypes was recognized, representing several nonsynonymous substitutions (30 SNPs) within the diverse regions of GBSSII (Figure 1).…”

“…However, several different functional alleles or haplotypes [12][13][14] have been identified in the waxy gene (GBSSI) region and are associated with amylose content in rice and many other crops, such as maize [15], wheat [16], barley [17], and cassava [18,19], but research on the functional properties of GBSSII gene in crops is limited, particularly in rice. A recent study reported novel GBSSII haplotypes in rice through genome-wide identification and genetic variation analyses [20], but additional evolutionary analyses on this gene have not been performed. Evolutionary insights based on SNP haplotypes of many starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb) other than GBSSII have been provided by the high variability between cultivated and wild rice populations [21].…”

Functional analysis of the eTM-miR171-SCL6 module regulating somatic embryogenesis in Lilium pumilum DC. Fisch

“…Starch synthase (SS) includes granule-bound starch synthase (GBSS) and soluble starch synthase (SSS). GBSS mainly catalyzes the synthesis of amylose, and SSS mainly catalyzes the synthesis of amylopectin [ 52 ]. α-Amylase (AMY) and β-amylase (BAM) are key enzymes in starch degradation [ 53 ].…”