scholarly journals Genome‐wide SNP discovery and QTL mapping for economic traits in a recombinant inbred line of Oryza sativa

2021 ◽  
Author(s):  
Gengmi Li ◽  
Qianhua Yang ◽  
Deqiang Li ◽  
Tao Zhang ◽  
Li Yang ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Qtl Mapping ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Snp Discovery ◽  
Economic Traits ◽  
Genome Wide

QTL mapping of resistance to powdery mildew race 1 in a recombinant inbred line population of melon

Plant Disease ◽  
2021 ◽  
Author(s):  
Sandra Branham ◽  
Chandrasekar S Kousik ◽  
Mihir Mandal ◽  
Patrick Wechter
Keyword(s):  
South Carolina ◽  
Powdery Mildew ◽  
Qtl Mapping ◽  
Candidate Genes ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Missense Mutations ◽  
Race 1 ◽  
Whole Genome Resequencing

Powdery mildew, caused by the fungus Podosphaera xanthii, is one of the most important diseases of melon. While there are several pathogenic races of P. xanthii, race 1 is the predominant race in South Carolina and the U.S. We used a densely genotyped recombinant inbred line melon population for traditional QTL mapping, to identify two major (qPx1-5 and qPx1-12) and two minor (qPx1-4 and qPx1-10) QTLs (named according to race – chromosome number) associated with resistance to P. xanthii race 1. QTL mapping of disease severity in multiple tissues (hypocotyl, cotyledons, true leaves and stems) identified the same genetic basis of resistance in all tissue types. Whole-genome resequencing of the parents was used for marker development across the major QTLs and functional annotation of SNPs for candidate gene analysis. KASP markers were tightly linked to the QTL peaks of qPx1-5 (pm1-5_25329892, pm1-5_25461503 and pm1-5_25625375) and qPx1-12 (pm1-12_22848920 and pm1-12_22904659) in the population and will enable efficient marker-assisted introgression of powdery mildew resistance into improved germplasm. Candidate genes were identified in both major QTL intervals that encode putative R genes with missense mutations between the parents. The candidate genes provide targets for future breeding efforts and a fundamental examination of resistance to powdery mildew in melon.

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

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.

QTL mapping of grain arabinoxylan contents in common wheat using a recombinant inbred line population

Euphytica ◽  
2015 ◽  
Vol 208 (2) ◽  
pp. 205-214 ◽  
Author(s):  
Li Yang ◽  
Dehui Zhao ◽  
Jun Yan ◽  
Yelun Zhang ◽  
Xianchun Xia ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Common Wheat ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred Line Population ◽  
Recombinant Inbred

scholarly journals QTL Mapping for Drought-Responsive Agronomic Traits Associated with Physiology, Phenology, and Yield in an Andean Intra-Gene Pool Common Bean Population

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 225
Author(s):  
Aleš Sedlar ◽  
Mateja Zupin ◽  
Marko Maras ◽  
Jaka Razinger ◽  
Jelka Šuštar-Vozlič ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Qtl Mapping ◽  
Common Bean ◽  
Linkage Map ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Gene Pool ◽  
Agronomic Traits ◽  
Drought Response

Understanding the genetic background of drought tolerance in common bean (Phaseolus vulgaris L.) can aid its resilience improvement. However, drought response studies in large seeded genotypes of Andean origin are insufficient. Here, a novel Andean intra-gene pool genetic linkage map was created for quantitative trait locus (QTL) mapping of drought-responsive traits in a recombinant inbred line population from a cross of two cultivars differing in their response to drought. Single environment and QTL × environment analysis revealed 49 QTLs for physiology, phenology, and yield-associated traits under control and/or drought conditions. Notable QTLs for days to flowering (Df1.1 and Df 1.2) were co-localized with a putative QTL for days to pods (Dp1.1) on linkage group 1, suggesting pleiotropy for genes controlling them. QTLs with stable effects for number of seeds per pod (Sp2.1) in both seasons and putative water potential QTLs (Wp1.1, Wp5.1) were detected. Detected QTLs were validated by projection on common bean consensus linkage map. Drought response-associated QTLs identified in the novel Andean recombinant inbred line (RIL) population confirmed the potential of Andean germplasm in improving drought tolerance in common bean. Yield-associated QTLs Syp1.1, Syp1.2, and Sp2.1 in particular could be useful for marker-assisted selection for higher yield of Andean common beans.

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