Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia

Abstract

Rice double-haploid (DH) lines of an indica and japonica cross were grown at nine different locations across four countries in Asia. Genotype-by-environment (G x E) interaction analysis for 11 growth- and grain yield-related traits in nine locations was estimated by AMMI analysis. Maximum G x E interaction was exhibited for fertility percentage number of spikelets and grain yield. Plant height was least affected by environment, and the AMMI model explained a total of 76.2% of the interaction effect. Mean environment was computed by averaging the nine environments and subsequently analyzed with other environments to map quantitative trait loci (QTL). QTL controlling the 11 traits were detected by interval analysis using mapmaker/qtl. A threshold LOD of >/=3.20 was used to identify significant QTL. A total of 126 QTL were identified for the 11 traits across nine locations. Thirty-four QTL common in more than one environment were identified on ten chromosomes. A maximum of 44 QTL were detected for panicle length, and the maximum number of common QTL were detected for days to heading detected. A single locus for plant height (RZ730-RG810) had QTL common in all ten environments, confirming AMMI results that QTL for plant height were affected the least by environment, indicating the stability of the trait. Two QTL were detected for grain yield and 19 for thousand-grain weight in all DH lines. The number of QTL per trait per location ranged from zero to four. Clustering of the QTL for different traits at the same marker intervals was observed for plant height, panicle number, panicle length and spikelet number suggesting that pleiotropism and or tight linkage of different traits could be the possible reason for the congruence of several QTL. The many QTL detected by the same marker interval across environments indicate that QTL for most traits are stable and not essentially affected by environmental factors.

NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars

“…In this region, where SPIKE was identified, several QTLs for TSN have been detected, among which the alleles from japonica or tropical japonica cultivars increased TSN (30)(31)(32)(33)(34)(35)(36)(37)(38). Hitherto, no gene for TSN or grain yield in this cluster has been isolated (39).…”

Substitution Mapping of dth1.1, a Flowering-Time Quantitative Trait Locus (QTL) Associated With Transgressive Variation in Rice, Reveals Multiple Sub-QTL

“…A comparative QTL analysis of rice heading-date QTL on the short arm of chromosome 1 reveals several other published QTL in the same region as dth1.1. Of 17 rice QTL studies examined Xiao et al 1995Xiao et al , 1996Xiao et al , 1998Kohn et al 1997;Lu et al 1997;Yano et al 1997;Doi et al 1998;Lin et al 1998;Xiong et al 1999;Maheswaran et al 2000;Bres-Patry et al 2001;Moncada et al 2001;Cai and Morishima 2002;Yu et al 2002;Hittalmani et al 2003;Septiningsih et al 2003), five heading-date QTL were identified in the dth1.1 region, four of which were detected in interspecific crosses in rice (Kohn et al 1997;Doi et al 1998;Xiao et al 1998;Cai and Morishima 2002) and one in an intraspecific cross (Maheswaran et al 2000). Interestingly, in the thoroughly studied intraspecific Nipponbare/Kasalath population, 14 heading-date QTL have been identified, none of which are located on chromosome 1 (Yano 2001).…”

Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

“…A total of 80 QTLs for flowering time detected under well-watered conditions were collected from ten papers (Li et al 1995;Yano et al 1997;Lafitte and Courtois 1999;Lin et al 2000;Maheswaran et al 2000;Yamamoto et al 2000;Yu et al 2002;Hittalmani et al 2003;Lanceras et al 2004;Dong et al 2004). A total of 59 QTLs for plant height were collected from ten papers (Li et al 1995;Lafitte and Courtois 1999;Hemamalini et al 2000;Yu et al 2002;Courtois et al 2003;Hittalmani et al 2003;Lanceras et al 2004;Xu et al 2004;MacMillan et al 2006;Gomez et al 2006). All the QTLs are compiled in TropgeneDB.…”