Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

Abstract

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars.

Alleles Affecting 30 Traits for Productivity in Two Japonica Rice Varieties, Koshihikari and Nipponbare (Oryza sativaL.)

“…In BILs between Koshihikari and Nipponbare, the number of days to heading has been correlated with 33 traits, including yield, plant height, and flag leaf area (Hori et al, 2012). Similar results have been reported for a number of traits on various genetic materials (Mei et al, 2003;Kwon et al, 2008;Takeuchi et al, 2008).…”

“…For the fifteen traits, total 37 overlapping among QTLs or CRATs were detected. Almost one third part of QTLs that was detected in BILs between Nipponbare and Koshihikari overlapped with CRATs in Kos-Nip CSSLs (Hori et al, 2012). Similarly, ratios of overlap with our CRATs were 10% or 20% in the CRATs by Kasalath and Nona Bokra alleles, respectively.…”

“…The main cause of these results was that heading date strongly affected other traits. According to Hori et al (2012), most QTLs for agronomic traits are located near 2 QTLs associated with the number of days to heading. In this study, days to heading was correlated with 7 traits in KosNip and 2 in Nip-Kos (data not shown; threshold level P < 0.001), and accounted for less than 13% and 5%, respectively, of all correlations detected in this study.…”

“…Corresponding CRATs with contrasting effects were not detected in the diameter at the panicle neck (+18%). We compared chromosomal positions of CRATs for 22 traits with those of QTLs or CRATs in four previous reports (Table 1) (Madoka et al, 2008;Hori et al, 2012;Ujiie et al, 2012;Ujiie and Ishimaru, 2013). For the fifteen traits, total 37 overlapping among QTLs or CRATs were detected.…”

“…These CSSLs are useful for prompt and easy narrowing of candidate genes based on the genomic information. Between Nipponbare and Koshihikari, quantitative trait loci (QTL) analysis for 50 agronomic traits has been conducted using backcross inbred lines (BILs) (Hori et al, 2012). However, most of these traits are strongly influenced by heading date, and thus the existence and performance of Nipponbare alleles on a Koshihikari background could not be detected using this BILs.…”