Mapping quantitative trait loci (QTL) for grain size in rice using a RIL population from Basmati × indica cross showing high segregation distortion

Feng, J., Hwang, R., Chang, K. F., Conner, R. L., Hwang, S. F., Strelkov, S. E., Gossen, B. D., McLaren, D. L. and Xue, A. G. 2011. Identification of microsatellite markers linked to quantitative trait loci controlling resistance to Fusarium root rot in field pea. Can. J. Plant Sci. 91: 199–204. Fusarium root rot, caused by Fusarium solani (Mart.) Sacc. f. sp. pisi (F. R. Jones) W. C. Snyder & H. N. Hans, is the most common root disease of field pea (Pisum sativum L.) in western Canada. In this study, a recombinant inbred line (RIL) population (n=71) of field pea, derived from crosses between a resistant cultivar Carman, and a susceptible cultivar Reward, was evaluated to identify quantitative trait loci (QTL) controlling resistance to Fusarium root rot. The parental genotypes and RILs were evaluated for resistance to root rot following inoculation with F. solani in field experiments during 2007 and 2008. The frequency distribution of disease severities among the RILs was continuous. Transgressive segregation for resistance was observed among the RILs, with five lines more resistant than Carman, but no lines were more susceptible than Reward. To identify DNA markers linked with the resistance, 213 microsatellite markers were screened with genomic DNA from the two parental cultivars. Only 14 markers were polymorphic between the two parents and were used to genotype each of the RILs. Quantitative trait loci analysis based on the mean disease severity data from 2007 and 2008 identified a QTL that explained 39.0% of the phenotypic variance in the RIL population. This QTL is flanked by markers AA416 and AB60 on linkage group VII. The microsatellite markers that are closely linked to this QTL may be useful for marker assisted selection to develop cultivars with superior Fusarium root rot resistance.

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Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.)

Canadian Journal of Plant Science ◽

10.4141/cjps-2015-091 ◽

2015 ◽

Vol 95 (6) ◽

pp. 1133-1144

Author(s):

R. Khanal ◽

A. Navabi ◽

L. Lukens

Keyword(s):

Quantitative Trait Loci ◽

Qtl Mapping ◽

Linkage Map ◽

Inbred Line ◽

Recombinant Inbred Line ◽

Quantitative Trait ◽

Recombinant Inbred ◽

Map Construction ◽

Ril Population ◽

Trait Loci

Khanal, R., Navabi, A. and Lukens, L. 2015. Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.). Can. J. Plant Sci. 95: 1133–1144. Intermating of individuals in an F2 population increases genetic recombination between markers, which is useful for linkage map construction and quantitative trait loci (QTL) mapping. The objectives of this study were to compare the linkage maps and precision of QTL detection in an intermated recombinant inbred line (IRIL) population and a selfed recombinant inbred line (RIL) population. Both, IRIL and RIL, populations were developed from Zea mays inbred lines CG60 and CG102. The populations were grown in two environments to evaluate traits, and inbred lines from each population were genotyped with SSR and SNP markers for linkage map construction and QTL identification. In addition, we simulated RIL and IRIL populations from two inbred parents to compare the precision of QTL detection between simulated RIL and IRIL populations. In the empirical study, the linkage map was longer in RIL as compared with IRIL, and the average QTL support interval was reduced by 1.37-fold in the IRIL population compared with the RIL population. We detected 16 QTL for flowering time, plant height, leaf number, and stay green in at least one recombinant inbred line population. Two out of 16 QTL were shared between two recombinant inbred line populations. In the simulation study, the QTL support interval was reduced by 1.66-fold in the IRIL population as compared with the RIL population and linked QTL were identified more frequently in IRIL population as compared with RIL population. This study supports the utility of intermated RIL populations for precise QTL mapping.

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Genetic Analysis of Recombinant Inbred Lines for Sorghum bicolor × Sorghum propinquum

G3 Genes|Genome|Genetics ◽

10.1534/g3.112.004499 ◽

2013 ◽

Vol 3 (1) ◽

pp. 101-108 ◽

Cited By ~ 21

Author(s):

Wenqian Kong ◽

Huizhe Jin ◽

Cleve D Franks ◽

Changsoo Kim ◽

Rajib Bandopadhyay ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Sorghum Bicolor ◽

Genetic Map ◽

Quantitative Trait ◽

Recombinant Inbred ◽

Growth And Development ◽

Recombinant Inbred Lines ◽

Sorghum Propinquum ◽

Ril Population ◽

Trait Loci

Abstract We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor × Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor × S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map has DNA marker density well-suited to quantitative trait loci mapping and samples most of the genome, our previous observations that sorghum pericentromeric heterochromatin is recalcitrant to recombination is highlighted by the finding that the vast majority of recombination in sorghum is concentrated in small regions of euchromatin that are distal to most chromosomes. The advancement of the RIL population in an environment to which the S. bicolor parent was well adapted (indeed bred for) but the S. propinquum parent was not largely eliminated an allele for short-day flowering that confounded many other traits, for example, permitting us to map new quantitative trait loci for flowering that previously eluded detection. Additional recombination that has accrued in the development of this RIL population also may have improved resolution of apices of heterozygote excess, accounting for their greater abundance in the F5 than the F2 generation. The S. bicolor × S. propinquum RIL population offers advantages over early-generation populations that will shed new light on genetic, environmental, and physiological/biochemical factors that regulate plant growth and development.

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Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat × wild emmer wheat RIL population

Theoretical and Applied Genetics ◽

10.1007/s00122-009-1044-z ◽

2009 ◽

Vol 119 (2) ◽

pp. 353-369 ◽

Cited By ~ 145

Author(s):

Zvi Peleg ◽

Ismail Cakmak ◽

Levent Ozturk ◽

Atilla Yazici ◽

Yan Jun ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Durum Wheat ◽

Quantitative Trait ◽

Wild Emmer Wheat ◽

Emmer Wheat ◽

Wild Emmer ◽

Mineral Nutrient ◽

Nutrient Concentrations ◽

Ril Population ◽

Trait Loci

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Quantitative Trait Loci and Candidate Gene Identification for Chlorophyll Content in RIL Rice Population under Drought Conditions

Indonesian Journal of Natural Pigments ◽

10.33479/ijnp.2021.03.2.54 ◽

2021 ◽

Vol 3 (2) ◽

pp. 54

Author(s):

Yheni Dwiningsih ◽

Anuj Kumar ◽

Julie Thomas ◽

Charlez Ruiz ◽

Jawaher Alkahtani ◽

...

Keyword(s):

Drought Stress ◽

Quantitative Trait Loci ◽

Grain Yield ◽

Candidate Genes ◽

Chlorophyll Content ◽

Quantitative Trait ◽

Flag Leaf ◽

Drought Condition ◽

Ril Population ◽

Trait Loci

Rice (Oryza sativa) is the staple food for more than half of the world population. Rice needs 2-3 times more water compared to other crops. Drought condition is one of the limited factor in rice production. Recombinant inbred line population derived from a cross between rice genotype tropical japonica Kaybonnet and indica ZHE733 named K/Z RIL population was used to identify candidate genes for chlorophyll content related to grain yield under drought condition. Chlorophyll content in the flag leaf of the rice plant is related to the grain yield since chlorophyll plays an important role in the photosynthesis. The K/Z RIL population was screened in the field at Fayetteville, Arkansas, USA by controlled drought stress treatment at the reproductive stage (R3), and the effect of drought stress was quantify by measuring chlorophyll content, flag leaf characteristics, and grain yield. Quantitative trait loci (QTL) analysis was performed with a set of 4133 single nucleotide polymorphism (SNP) markers by using QTL IciMapping software version 4.2.53. Candidate genes within the QTL regions were identified by using the MSU Rice Genome Annotation Project database release 7.0 as the reference. A total of eleven QTLs and forty-three candidate genes were identified for chlorophyll content related to the grain yield under drought condition. Most of the candidate genes involve in biological processes, molecular functions, and cell components. By understanding the genetic complexity of the chlorophyll content, this research provides information to develop drought-resistant rice varieties with greater productivity under drought stress condition.

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