Detecting quantitative trait loci for water use efficiency in rice using a recombinant inbred line population

Zhou, Guangsheng; Liu, Fang; Cao, Jianhua; Yue, Bing; Xiong, Lizhong

doi:10.1007/s11434-011-4444-9

Cited by 7 publications

(5 citation statements)

References 24 publications

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“…QTLs identified with small effects also contributed to the genetic control of complex polygenic traits. Small-effect QTLs for complex traits are highly polygenic in nature and have been reported in many crops, including maize [ 50 ] and rice [ 51 ]. Indeed, the contribution of each locus may be negligible, but the total contribution is usually significant for such complex traits.…”

Section: Discussionmentioning

confidence: 99%

Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut

Pandey

Gangurde

Sharma

et al. 2020

Genes

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A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2.2 cM distance between loci in the recombinant inbred line (TAG 24 × ICGV 86031) population using high-density 58K single nucleotide polymorphism (SNP) “Axiom_Arachis” array. Quantitative trait locus (QTL) analysis was performed using extensive phenotyping data generated for 20 drought tolerance- and two iron deficiency tolerance-related traits from eight seasons (2004–2015) at two locations in India, one in Niger, and one in Senegal. The genome-wide QTL discovery analysis identified 19 major main-effect QTLs with 10.0–33.9% phenotypic variation explained (PVE) for drought tolerance- and iron deficiency tolerance- related traits. Major main-effect QTLs were detected for haulm weight (20.1% PVE), SCMR (soil plant analytical development (SPAD) chlorophyll meter reading, 22.4% PVE), and visual chlorosis rate (33.9% PVE). Several important candidate genes encoding glycosyl hydrolases; malate dehydrogenases; microtubule-associated proteins; and transcription factors such as MADS-box, basic helix-loop-helix (bHLH), NAM, ATAF, and CUC (NAC), and myeloblastosis (MYB) were identified underlying these QTL regions. The putative function of these genes indicated their possible involvement in plant growth, development of seed and pod, and photosynthesis under drought or iron deficiency conditions in groundnut. These genomic regions and candidate genes, after validation, may be useful to develop molecular markers for deploying genomics-assisted breeding for enhancing groundnut yield under drought stress and iron-deficient soil conditions.

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Section: Discussionmentioning

confidence: 99%

Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut

Pandey

Gangurde

Sharma

et al. 2020

Genes

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“…Currently, QTL mapping has been applied for crop improvement (Kumar and Kumar, 2009), and a large number of molecular markers linked with traits have been obtained; moreover, some QTLs controlling agronomic traits have been successfully cloned (Zhou et al, 2011). In maize, numerous QTLs have been identified that control agronomic traits, and these QTLs have been mapped to 10 chromosomes in maize (Tsonev et al, 2009;Qiu et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…In comparison, the recombinant inbred line (RIL) population is immortal and can be used in different regions and times because it consists of homogenous individuals. The RIL population has been widely used for QTL mapping in crops (Balint-Kurti et al, 2008;Du et al, 2009;Blair et al, 2010;Zhou et al, 2011), but it has rarely been used for QTL mapping for traits associated with plant architecture in maize (Tang et al, 2007;Liu et al, 2010). Additionally, the same type of segregating population derived from different parental lines likely provide different QTL identification results, including different location, number, and genetic effects.…”

Section: Introductionmentioning

confidence: 99%

Genetic analysis of agronomic traits associated with plant architecture by QTL mapping in maize

Zheng

Liu²

2013

Genet. Mol. Res.

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ABSTRACT. Maize (Zea mays L.) is one of the most important cereal crops worldwide, and increasing the grain yield and biomass has been among the most important goals of maize production. The plant architecture can determine the grain yield and biomass to some extent; however, the genetic basis of the link between the plant architecture and grain yield/biomass is unclear. In this study, an immortal F 9 recombinant inbred line population, derived from the cross Mo17 x Huangzao4, was used to detect quantitative trait loci (QTLs) for 3 traits associated with plant architecture under two nitrogen regimes: plant height, ear height, and leaf number. As a result, 8 and 10 QTLs were identified under the high nitrogen regime and low nitrogen regime, respectively. These QTLs mapped to chromosomes 1 (six QTLs), 2 (one QTL), 3 (one QTL), 7 (two QTLs), and 9 (eight QTLs), and had different genetic distances to their closest markers, ranging from 0 to 22.0 cM, explaining 4.7 to 20.5% of the phenotypic variance. Because of an additive effect, 9 and 9 could make the phenotypic values of traits increase and decrease to some extent, respectively. These results are beneficial for understanding the genetic basis of agronomic traits associated with plant architecture and for performing marker-assisted selection in maize breeding programs.

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“…The PVE of these M-QTLs were low indicating minor effect QTLs. Small-effect QTLs for complex traits such as yield were also been identified in rice ( Oryza sativa L.) (Zhou et al 2011 ) and maize ( Zea mays L.) (Ribaut et al 1997 ). These results confirm the current understanding that the complex traits are highly polygenic in nature and are the outcome of several small-effect genetic factors.…”

Section: Discussionmentioning

confidence: 99%

Identification of quantitative trait loci for yield and yield related traits in groundnut (Arachis hypogaea L.) under different water regimes in Niger and Senegal

et al. 2015

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Yield under drought stress is a highly complex trait with large influence to even a minor fluctuation in the environmental conditions. Genomics-assisted breeding holds great promise for improving such complex traits more efficiently in less time, but requires markers associated with the trait of interest. In this context, a recombinant inbred line mapping population (TAG 24 × ICGV 86031) was used to identify markers associated with quantitative trait loci (QTLs) for yield and yield related traits at two important locations of West Africa under well watered and water stress conditions. Among the traits analyzed under WS condition, the harvest index (HI) and the haulm yield (HYLD) were positively correlated with the pod yield (PYLD) and showed intermediate broad sense heritability. QTL analysis using phenotyping and genotyping data resulted in identification of 52 QTLs. These QTLs had low phenotypic variance (<12 %) for all the nine traits namely plant height, primary branching, SPAD chlorophyll meter reading, percentage of sound mature kernels, 100 kernel weight, shelling percentage, HI, HYLD and PYLD. Interestingly, few QTLs identified in this study were also overlapped with previously reported QTLs detected for drought tolerance related traits identified earlier in Indian environmental conditions using the same mapping population. Accumulating these many small-effect QTLs into a single genetic background is nearly impossible through marker-assisted backcrossing and even marker-assisted recurrent selection. Under such circumstances, the deployment of genomic selection is the most appropriate approach for improving such complex traits with more precision and in less time.Electronic supplementary materialThe online version of this article (doi:10.1007/s10681-015-1472-6) contains supplementary material, which is available to authorized users.

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Detecting quantitative trait loci for water use efficiency in rice using a recombinant inbred line population

Cited by 7 publications

References 24 publications

Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut

Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut

Genetic analysis of agronomic traits associated with plant architecture by QTL mapping in maize

Identification of quantitative trait loci for yield and yield related traits in groundnut (Arachis hypogaea L.) under different water regimes in Niger and Senegal

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