Soluble starch synthase IVa determines cooked rice elongation in waxy and non-waxy rices (Oryza sativa L.)

Cooked rice elongation (CRE) is an attractive grain quality reported only in Basmati from India and Pakistan and in Paw San Hmwe from Myanmar. Several reports on the discovery of genes controlling CRE were unequivocal in rice. Here, we design new experiments to uncover genes that significantly affect CRE in waxy and non-waxy rice varieties.

We created 105 BC₁F₂ lines derived from a cross between a high-CRE waxy rice, NHN, and Pink+4 (#20A09), a low-CRE, low-glycemic-index, non-waxy rice, to generate two distinct phenotypic pools for QTL-seq analysis: high-CRE and low-CRE. 31 waxy, non-waxy, and pigmented rice varieties, including a few Basmati accessions, were the test panel for the identified single-nucleotide polymorphic markers (SNPs) developed from the candidate gene.

Six significant QTLs, localized by ΔSNP Indexes, were mapped on chromosomes 1 (qCRE1), 4 (qCRE4), 7 (qCRE7), 10 (qCRE10.1, qCRE10.2) and 12 (qCRE12). Significantly, the qCRE1, which spans 29.3-30.2 Mb, showed the strongest ΔSNP Index with a significant phenotypic variance explained (PVE), whereas qCRE4, qCRE7, qCRE10.1, qCRE10.2 and qCRE12 were non-significant. Specifically, SNP-SSIVa_1_30038156 (R01030038156), a non-synonymous mutation encoding the A-to-G variant in exon 5 that strongly discriminated between low and high-CRE in waxy, is co-localised in the exon 5 of the Soluble Starch Synthase IVa (SSIVa) on qCRE1. In this critical region, data mining identified 14 informative SNPs in the coding and non-coding sequence of the SSIVa gene. Moreover, four haplotypes (HAP) derived from seven informative SNPs in SSIVa correctly classified the rice accessions into the extra-CRE (HAP1), high-CRE (HAP2), and low-CRE (HAP 3 and 4). All extra-CRE rice varieties, including 11 Basmati and Paw San Hmwe, were classified in HAP1. While high-CRE rice varieties, including NHN and six rice varieties, were designated in HAP2. 13 low-CRE rice varieties were classified in either HAP3 or HAP4.

For the first time, this finding signifies the genetic impact of SSIVa on CRE in both waxy and non-waxy rice varieties. The corresponding haplotypic DNA markers will benefit rice breeders aiming to improve elite rice varieties with attractive cooked-rice elongation through marker-assisted selection.