Identification of QTLs and candidate genes for days to heading in an upland New Rice for Africa (NERICA) variety

Abstract

To produce rice varieties adaptable to unfavorable environments in Africa, New Rice for Africa (NERICA) varieties have been developed by inter-specific crossings. The basic idea of NERICA was to combine the useful characteristics of the African rice species Oryza glaberrima and an Asian rice species, Oryza sativa. However, the genetic basis of the agronomic characteristics of NERICA varieties is not fully understood. We performed a QTL analysis to examine the genetic basis of days to heading (DTH) in an upland variety, NERICA10. We found that NERICA10 had weaker photoperiod sensitivity (PS) and shorter DTH under long day-length conditions than its parental varieties. We then examined QTLs controlling DTH under natural long-day-length conditions by using segregating populations. We found three QTLs for DTH, on chromosomes 4, 6, and 8. Among them, qDTH8.1, located on chromosome 8, had the strongest effect. By comparing nucleotide sequences, we found that NERICA10 had a loss of the functional allele of DTH8, which was located in the candidate region of qDTH8.1. These results suggested that loss of function of DTH8 is the causal factor of weakened PS in NERICA10. The information on these QTLs will be useful for improving rice varieties for better adaption to African conditions.