Mapping of QTL for Three Panicle Exsertion-Related Traits in Rice Under Different Growing Environments

Panicle exclosure in cytoplasmic male sterility (CMS) line is highly correlated with outcrossing rate of CMS in hybrid rice (Oryza sativa L.) seed production. Panicle enclosure occurs when flag leaf sheath length exceeds the uppermost internode length. To improve panicle exsertion, 98 backcross inbred lines (BILs), derived from a backcross of Nipponbare (japonica)/Kasalath (indica)//Nipponbare by the single seed descent method, were planted in 3 growing environments to disclose the genetic mechanism of flag leaf sheath length, the uppermost internode length, and panicle enclosure. At 5% of genome-wide type I error, QTLs of the 3 traits by Composite Interval Mapping (CIM) method were detected. Three of them, located on chromosomes 1, 3, and 4, were for flag leaf sheath length. They explained the phenotypic variances by 12.8–18.5%. The QTL, qFLL-1, was detected in all the 3 environments, whose positive allele was from Nipponbare. The QTLs, qFLL-3 and qFLL-4, were detected in a single environment with positive alleles from Kasalath. For the uppermost internode length, 3 QTLs were detected on chromosomes 1, 3, and 6. They explained 5.6–14.2% of the phenotypic variances. Among them, qUIL-6 was detected in all the 3 environments, and Nipponbare donated the positive allele in the locus. The other 2 QTLs were detected in 2 environments, and Kasalath carried the positive allele. Four QTLs for panicle enclosure length were located on chromosomes 1, 3, 5, and 10, which explained 6.8–17.8% of the phenotypic variances. Among them, qPEL-10 and qPEL-5 were detected in 3 and 2 environments, respectively, whereas the other 2 QTLs, qPEL-1 and qPEL-3, were only in a single environment. The positive alleles of qPEL-10 and qPEL-5 originated from Nipponbare, and the positive alleles of qPEL-1 and qPEL-3 were donated by Kasalath.