Dissecting the quantitative variations of threshability in rice (Oryza sativa L.)

Abstract

In rice, low threshability retains grains on the panicles especially in japonica rice (O. sativa subsp. Japonica) and high threshability makes it easier for harvesting in indica. The genetic mechanisms underlying moderate threshability in rice remain largely unclear. A set of reciprocal Backcross Inbred Lines BILs including 226 and 229 lines from indica rice (O. sativa subsp. indica) and japonica rice (O. sativa subsp. japonica) backgrounds, respectively, and 262   recombinant inbred lines RILs developed from same cross between an indica, were adopted for testing threshability in two seasons. Percentages of dislodged grains were estimated at the maturity, harvesting and after sun drying. A total of 265 SNP markers developed based on sequencing and evenly distributed throughout the 12  chromosomes were used for genotyping assay. Inclusive composite interval mapping (ICIM) was used to dissect genomic regions and interactions affecting quantitative variation of threshability. A total of 13 QTLs were found to be conferring  quantitative variations of threshability, which were distributed on all chromosomes. Two known major genes (QTLs) qSH1 and sh4 were also present. New additive QTLs, qThr1-a, qThr2, qThr3 qThr7, qThr8, qThr10, qThr11 and  qThr12 were found as well. Twenty-four epistatics QTLs of which eight were common in both japonica and indica backgrounds were detected in two consecutive seasons. The overall threshability explained by all additive and interacting QTLs (R2) were 70% and 1 for indica, 15 and 8% for japonica and 17.4 and 10.6% for RIL backgrounds, respectively. Findings have preliminarily revealed a relatively complex mechanism underlying the quantitative variations of threshability in rice, which was controlled not only by major loci but also affected by epistasis and genetic background effects.

Key words: epistasis, genetic background effect, quantitative variation, rice (Oryza sativa L.), threshability