QTL × environment interactions in rice. I. Heading date and plant height

Abstract

One hundred twenty six doubled-haploid (DH) rice lines were evaluated in nine diverse Asian environments to reveal the genetic basis of genotype x environment interactions (GEI) for plant height (PH) and heading date (HD). A subset of lines was also evaluated in four water-limited environments, where the environmental basis of G x E could be more precisely defined. Responses to the environments were resolved into individual QTL x environment interactions using replicated phenotyping and the mixed linear-model approach. A total of 37 main-effect QTLs and 29 epistatic QTLs were identified. On average, these QTLs were detectable in 56% of the environments. When detected in multiple environments, the main effects of most QTLs were consistent in direction but varied considerably in magnitude across environments. Some QTLs had opposite effects in different environments, particularly in water-limited environments, indicating that they responded to the environments differently. Inconsistent QTL detection across environments was due primarily to non- or weak-expression of the QTL, and in part to significant QTL x environment interaction effects in the opposite direction to QTL main effects, and to pronounced epistasis. QTL x environment interactions were trait- and gene-specific. The greater GEI for HD than for PH in rice were reflected by more environment-specific QTLs, greater frequency and magnitude of QTL x environment interaction effects, and more pronounced epistasis for HD than for PH. Our results demonstrated that QTL x environment interaction is an important property of many QTLs, even for highly heritable traits such as height and maturity. Information about QTL x environment interaction is essential if marker-assisted selection is to be applied to the manipulation of quantitative traits.

Identification of Quantitative Trait Loci Controlling Symptom Development During Viral Infection inArabidopsis thaliana

“…The simplest explanation is that this could be due to environmental effect, since the populations were tested separately. Three types of QTL-environment interactions have been proposed to explain differential QTL detection while using at least one similar parent (Li et al 2003): i) some QTL are expressed in one environment and not in another, ii) QTL can be expressed more in one condition than in an other, or finally, iii) QTL can have opposite effects in two different environmental conditions. However, another explanation is that different genetic factors are polymorphic in the two crosses or that effects are dependent on genetic background.…”

Identification of Quantitative Trait Loci Across Recombinant Inbred Lines and Testcross Populations for Traits of Agronomic Importance in Rice

“…In the vicinity of ph1, two genes associated with plant height have been identified and isolated: one is the gibberellin biosynthetic gene OsGA3ox2 (Itoh et al 2001) and the other is the brassinosteroid biosynthetic gene D2 (Hong et al 2003). The same QTL of hd6a has been identified in four populations, including CNHZAU Zh97/Ming63 RI , IRRI IR64/Azu DH (Li et al 2003), JRGP Nip/Kas F 2 (Lin et al 1998), and NIAS Kosh/Kas BIL (Yamamoto et al 2001). One allele of the gene (Hd3a) has been cloned, which encodes a protein closely related to Arabidopsis FT (Kojima et al 2002).…”

Quantitative Trait Loci for Grain Yield and Adaptation of Durum Wheat (Triticum durum Desf.) Across a Wide Range of Water Availability

“…Epistasis at the main QTL on chrs. 2BL and 3BS: Epistasis has great relevance for the outcome of markerassisted breeding Li et al 2003;Blanc et al 2006). Nevertheless, notable epistatic effects in wheat have been validated and analyzed in detail only for vernalization requirement (Yan et al 2006;Szucs et al 2007), a trait with a genetic basis less complex than that of GY.…”