Kernel elongation in rice

Genome-wide association study of cooking-caused grain expansion in rice (Oryza sativa L.)

Cooking-caused rice grain expansion (CCRGE) is a critical trait for evaluating the cooking quality of rice. Previous quantitative trait locus (QTL) mapping studies on CCRGE have been limited to bi-parental populations, which restrict the exploration of natural variation and mapping resolution. To comprehensively and precisely dissect the genetic basis of CCRGE, we performed a genome-wide association study (GWAS) on three related indices: grain breadth expansion index (GBEI), grain length expansion index (GLEI), and grain length-breadth ratio expansion index (GREI), using 345 rice accessions grown in two years (environments) and 193,582 SNP markers. By analyzing each environment separately using seven different methods (3VmrMLM, mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO), we identified a total of 32, 19 and 27 reliable quantitative trait nucleotides (QTNs) associated with GBEI, GLEI and GREI, respectively. Furthermore, by jointly analyzing the two environments using 3VmrMLM, we discovered 19, 22 and 25 QTNs, as well as 9, 5 and 7 QTN-by-environment interaction (QEIs) associated with GBEI, GLEI and GREI, respectively. Notably, 12, 9 and 15 QTNs for GBEI, GLEI and GREI were found within the intervals of previously reported QTLs. In the vicinity of these QTNs or QEIs, based on analyses of mutation type, gene ontology classification, haplotype, and expression pattern, we identified five candidate genes that are related to starch synthesis and endosperm development. The five candidate genes, namely, LOC_Os04g53310 (OsSSIIIb, near QTN qGREI-4.5s), LOC_Os05g02070 (OsMT2b, near QTN qGLEI-5.1s), LOC_Os06g04200 (wx, near QEI qGBEI-6.1i and QTNs qGREI-6.1s and qGLEI-6.1t), LOC_Os06g12450 (OsSSIIa, near QTN qGLEI-6.2t), and LOC_Os08g09230 (OsSSIIIa, near QTN qGBEI-8.1t), are predicted to be involved in the process of rice grain starch synthesis and to influence grain expansion after cooking. Our findings provide valuable insights and will facilitate genetic research and improvement of CCRGE.

A comparative evaluation of the effect of SSI and Wx allelic variation on rice grain quality and starch physicochemical properties

Near-isogenic lines Nip(Wx^b/SSI^j), Nip(Wx^b/SSIⁱ), Nip(wx/SSI^j) and Nip(wx/SSIⁱ) in the japonica rice Nipponbare (Nip) background containing allelic variation in the starch synthase gene SSI and Wx were investigated for cooked rice grain quality, starch morphology, pasting profiles, fine structure and crystallinity characteristics. Rice grains carrying the SSIⁱ allele had poor cooked rice taste in the Wx^b background. The introduction of SSIⁱ caused reduced cooked rice grain elongation, especially in the wx background. Starch granule size was reduced in SSIⁱ rice and the viscosity of flour and starch prepared from SSIⁱ rice was markedly increased. Moreover, analysis of the starch molecular structure revealed a remarkable increase in the short amylopectin chains and reduced starch relative crystallinity compared with SSI^j rice, which resulted in decreased gelatinization characteristics. These results suggest that SSI allelic variation has multiple effects on rice grain quality, as well as starch fine structure.

Mapping of QTLs conferring high grain length-breadth relative expansion during cooking in rice cultivar Paw San Hmwe

Paw San Hmwe (PSH) is a high-quality rice cultivar from Myanmar. PSH has short and broad grains, but the grains become slender after cooking. This desirable feature can be described as a high value of grain length-breadth relative expansion index (GREI). To understand the genetic basis of high GREI in PSH, we crossed PSH with Guang 8B (G8B), a rice cultivar from China with low GREI, to develop an F₂ population and a subsequent F_2:3 population. Based on the phenotypes of these two populations measured in two years and using the method of sequencing-based bulked segregant analysis followed by verification with conventional linkage-based QTL mapping method, we mapped three QTLs for GREI. The three QTLs were located on chromosomes 3, 5 and 12, respectively, with the trait-increasing alleles all from PSH, and could explain a total of 62.5% of the phenotypic variance and 84.1% of the additive genetic variance. The results suggest that the three QTLs would be useful for the genetic improvement of GREI in rice, and the linked markers will facilitate the selection of the favorable alleles from PSH in breeding.

Discovery and mapping of genomic regions governing economically important traits of Basmati rice

BACKGROUND

Basmati rice, originated in the foothills of Himalayas, commands a premium price in the domestic and international markets on account of its unique quality traits. The complex genetic nature of unique traits of Basmati as well as tedious screening methodologies involved in quality testing have been serious constraints to breeding quality Basmati. In the present study, we made an attempt to identify the genomic regions governing unique traits of Basmati rice.

RESULTS

A total of 34 Quantitative Trait Loci (QTLs) for 16 economically important traits of Basmati rice were identified employing F(2), F(3) and Recombinant Inbred Line (RIL) mapping populations derived from a cross between Basmati370 (traditional Basmati) and Jaya (semi-dwarf rice). Out of which, 12 QTLs contributing to more than 15 % phenotypic variance were identified and considered as major effect QTLs. Four major effect QTLs coincide with the already known genes viz., sd1, GS3, alk1 and fgr governing plant height, grain size, alkali spreading value and aroma, respectively. For the remaining major QTLs, candidate genes were predicted as auxin response factor for filled grains, soluble starch synthase 3 for chalkiness and VQ domain containing protein for grain breadth and grain weight QTLs, based on the presence of non-synonymous single nucleotide polymorphism (SNPs) that were identified by comparing Basmati genome sequence with that of Nipponbare.

CONCLUSIONS

To the best of our knowledge, the current study is the first attempt ever made to carry out genome-wide mapping for the dissection of the genetic basis of economically important traits of Basmati rice. The promising QTLs controlling important traits in Basmati rice, identified in this study, can be used as candidates for future marker-assisted breeding.