Molecular mapping of quantitative trait loci for grain chalkiness in rice (Oryza sativa L.)

Chalkiness of rice grain is an important but undesirable quality component, which has a profound influence on milling, cooking and eating qualities. Therefore, it is one of the key factors which determine the market value of rice grains. In this study, QTL mapping to determine the genomic regions governing percent grain with white core (PGWC) and chalkiness score (CS) was conducted using a population of 310 RILs, generated from the cross Pusa 1266/Jaya. Both the parents were extremely contrasting with Pusa 1266 with fully chalky and Jaya with translucent grains. RILs were evaluated at IARI, New Delhi during Khalif 2008 and 2009 and at RBGRC, Aduthurai during Rabi2009-10. Several QTL signals could be detected by single marker analysis. Among them, two QTLs, one each for PGWC and CS, were prominently detected by composite interval mapping between a marker interval RM 6273-RM204 on the short arm of chromosome 6. The QTL for PGWC, qPGWC6 was consistently detected during all the three seasons, explaining a phenotypic variation of 17.75%, 18.79% and 12.20% respectively. Similarly, the QTL for CS, qCS6 was also consistent across three seasons, accounting for a phenotypic variation of 24.3%, 24.75% and 24.03% respectively. Co-localization of both these QTLs may be representing a single genomic region, strongly implying the presence of Wx(b) locus in contributing to grain chalkiness of Pusa1266. The positive allele for the reduced grain chalkiness was contributed by Jaya. These results will be useful in fine mapping and validation of the identified QTLs.