Analysis of QTL×environment interaction for yield components and plant height in rice

Zhuang, Jie‐Yun; Lin, Hong‐Xuan; Lü, Jun; Qian, H.-R.; Hittalmani, Shailaja; Huang, Ning; Kangle, Zheng

doi:10.1007/s001220050628

Cited by 170 publications

(113 citation statements)

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“…One allele of the gene (Hd3a) has been cloned, which encodes a protein closely related to Arabidopsis FT (Kojima et al 2002). For five yield-related QTL (i.e., ppp2, spp1, gpp1, gw1, and gypp1), the same QTL have been reported in the corresponding chromosome regions in 5, 9, 3, 3, and 4 populations, respectively, among total 13 populations: CNHZAU Zh97/Ming63 RI (Cui et al 2002;Hua et al 2002Hua et al , 2003, CNHZAU Zhe97/Wuy2 (Jiang et al 2004), CNRRI Tes/CB (Zhuang et al 1997), CNRRI Zh97B/ Mil46 RI (Zhuang et al 2001(Zhuang et al , 2002, Cornell 9024/ LH422 RI (Xiao et al 1996), Cornell IR64/IRG105 (Septiningsih et al 2003), Cornell Jef/Oruf BC (Thomson et al 2003), HNAES MIL23/Aki RI (Yagi et al 2001), IGCAS ZYQ8/JX17 F 2 (Xu et al 1995), IRRI Lem/Teq RI (Mei et al 2003), IRRI Mil23/Aki RI (Nagata et al 2002;Kobayashi et al 2003), JRGP Nip/Kas F 2 (Yamaya et al 2002), and NIAS Kosh/Kas near isogenic lines (Obara et al 2004). Recently, the gene Gn1a, which produces more grains per panicle near the QTL gpp1 and encodes a cytokinin oxidase, has been cloned (Ashikari et al 2005).…”

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confidence: 60%

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

You

Jin

et al. 2006

Genetics

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This study was conducted to determine whether quantitative trait loci (QTL) controlling traits of agronomic importance detected in recombinant inbred lines (RILs) are also expressed in testcross (TC) hybrids of rice. A genetic map was constructed using an RIL population derived from a cross between B5 and Minghui 63, a parent of the most widely grown hybrid rice cultivar in China. Four TC hybrid populations were produced by crossing the RILs with three maintaining lines for the widely used cytoplasmic male-sterile (CMS) lines and the genic male-sterile line Peiai64s. The mean values of the RILs for the seven traits investigated were significantly correlated to those of the F 1 hybrids in the four TC populations. Twenty-seven main-effect QTL were identified in the RILs. Of these, the QTL that had the strongest effect on each of the seven traits in the RILs was detected in two or more of the TC populations, and six other QTL were detected in one TC population. Epistatic analysis revealed that the effect of epistatic QTL was relatively weak and cross combination specific. Searching publicly available QTL data in rice revealed the positional convergence of the QTL with the strongest effect in a wide range of populations and under different environments. Since the main-effect QTL is expressed across different testers, and in different genetic backgrounds and environments, it is a valuable target for gene manipulation and for further application in rice breeding. When a restorer line that expresses main-effect QTL is bred, it could be used in a number of cross combinations. H ETEROSIS has been very successfully exploited in diverse plants and animals. In agriculture, hybrid varieties contribute strongly worldwide to the production of many crop species, including the most important food crops, such as maize and rice (Stuber 1994;Yuan 1998;Khush 2001). Hybrid rice has a yield advantage of 15-20% over the best commercial rice varieties. The area planted to hybrid rice in China accounts for .50% of the total rice area of the country at present. The cultivation of hybrid rice has started on a large scale in many Asian countries.Several hypotheses have been proposed to explain the genetic basis of heterosis. The dominance hypothesis (Bruce 1910) proposes that dominant factors from either parent mask deleterious recessive mutations from the other parent in the heterozygous F 1 population. In contrast, the overdominance hypothesis (Shull 1908) holds that heterozygosity at single loci confers properties that are superior to either homozygote. The two hypotheses have been verified with molecular biology experiments (Stuber et al. 1992;Xiao et al. 1995). A third hypothesis suggests that heterosis may arise from epistasis between alleles at different loci (Yu et al. 1997;Goodnight 1999). More recently, further results have suggested that epistasis is the primary genetic basis of heterosis. It is suggested that separate efforts should be taken for breeding high-yielding inbred and hybrid cultivars in rice Luo et al. 2001)....

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confidence: 60%

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

You

Jin

et al. 2006

Genetics

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“…Stable QTL found in the present study may be due to one or combination of the following factors: (1) the stable QTL were responsible for major genetic effects and were associated with high LOD scores. As suggested by Tanksley (1993) and Zhuang et al (1997), QTL with major effects are more likely to be stable across multiple environments. (2) Highly heritable traits tend to be more repeatable and stable across multiple environments (Paterson et al, 1991).…”

Section: Discussionmentioning

confidence: 98%

“…Lu et al (1996) analyzed six important agronomic traits in rice through DH lines, and found that only 7 of 22 QTL were significant in all three environments. Zhuang et al (1997) analyzed yield components and plant height in rice F 2 lines, and the results suggested that only 17 of 44 QTLs were detected in more than one environment. These studies revealed that individual QTL was sensitive to the environment and QTL Â environment interaction played an important role in affecting quantitative traits.…”

Section: Discussionmentioning

confidence: 99%

QTL analyses of seed weight during the development of soybean (Glycine max L. Merr.)

Teng

Han

et al. 2008

Heredity

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At harvest traits such as seed weight are the sum of development and responses to stresses over the growing season and particularly during the reproductive phase of growth. The aim here was to measure quantitative trait loci (QTL) underlying the seed weight from early development to drying post harvest. One hundred forty-three F 5 derived recombinant inbred lines (RILs) developed from the cross of soybean cultivars 'Charleston' and 'Dongnong 594' were used for the analysis of QTL underlying mean 100-seed weight at six different developmental stages. QTL Â Environment interactions (QE) were analyzed by a mixed genetic mode based on 3 years' data. At an experiment-wise threshold of a ¼ 0.05 and by single-point analysis 94 QTL unaffected by QE underlay the mean seed weight at different developmental stages. Sixty-eight QTL affected by QE that also underlay mean seed weight were identified. From the 162 QTL 42 could be located on 12 linkage groups by composite interval mapping (LOD42.0). The numbers, locations and types of the QTL and the genetic effects were different at each developmental stage. On linkage group C2 the distantly linked QTL swC2-1, swC2-2 and swC2-3 each affected mean seed weight throughout the different developmental stages. The DNA markers linked to the QTL possessed potential for use in marker-assisted selection for soybean seed size. The identification of QTL with genetic main effects and QE interaction effects suggested that such interactions might significantly alter seed weight during seed development.

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“…QTL analysis has been used to study many agronomic traits in rice (Yano et al 1995, Lin et al 1996, Wu et al 1996, Xiao et al 1996, Zhuang et al 1997, Redoña and Mackill 1998, Xiao et al 1998, Moncada et al 2001. Although sterile spikelets were investigated in those reports, very few studies have dealt with the ripening percentage, which is important for determining economical grain yields.…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Loci for Sink Size and Ripening Traits in Rice (Oryza sativa L.).

et al. 2002

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Quantitative trait loci (QTLs) that affect sink size and ripening, which are often negatively correlated, were analyzed in two inbred lines of rice (Oryza sativa L.) derived from crosses between the semi-dwarf indica and japonica cultivars. Recombinant inbred lines (RILs) from Milyang23 (indica)/Akihikari (japonica), and back-crossed inbred lines (BCILs) from Sasanishiki (japonica)/Habataki(indica)//Sasanishiki///Sasanishiki were studied over a period of two years. A major QTL that was related to the number of spikelets per panicle was found in the same region of chromosome 1 in both populations. The indica allele increased the number of spikelets and reduced the ripening percentage. The indica allele of the QTL, which was found in both populations but at different locations on chromosome 6, also increased the number of spikelets per panicle, although to a lesser extent than in the case of the QTL on chromosome 1. In this instance, the number of spikelets per panicle did not have a negative effect on the ripening percentage. The increased number of spikelets produced by the QTL on chromosome 6 was due mainly to an increase in the number of primary rachis branches. In contrast, the effect of the QTL on chromosome 1 relied on an increase in the number of secondary rachis branches. In addition, dry matter production tended to increase when the QTL region of chromosome 6 belonged to the indica genotype. Therefore, both panicle structure and source productivity might contribute to the increase of the sink size without reducing the ripening percentage. We also found two loci on chromosomes 11 and 12 of the RILs that were associated with the percentage of incompletely filled spikelets, but which did not affect the sink size. It is considered that these QTLs could contribute significantly to the breeding of cultivars with increased sink size and increased ripening.

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Analysis of QTL×environment interaction for yield components and plant height in rice

Cited by 170 publications

References 9 publications

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

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

QTL analyses of seed weight during the development of soybean (Glycine max L. Merr.)

Quantitative Trait Loci for Sink Size and Ripening Traits in Rice (Oryza sativa L.).

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