scholarly journals A multi-parent recombinant inbred line population of Caenorhabditis elegans enhances mapping resolution and identification of novel QTLs for complex life-history traits

2018 ◽  
Author(s):  
Basten L. Snoek ◽  
Rita J.M. Volkers ◽  
Harm Nijveen ◽  
Carola Petersen ◽  
Philipp Dirksen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Life History ◽  
Caenorhabditis Elegans ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Qtl Analysis ◽  
Recombinant Inbred ◽  
Life History Traits ◽  
Rna Seq ◽  
Ril Population

AbstractLocal populations of the bacterivorous nematode Caenorhabditis elegans can be genetically almost as diverse as global populations. To investigate the effect of local genetic variation on heritable traits, we developed a new recombinant inbred line (RIL) population derived from four wild isolates. The wild isolates were collected from two closely located sites in France: Orsay and Santeuil. By crossing these four genetically diverse parental isolates a population of 200 RILs was constructed. RNA-seq was used to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the four genotypes with an average spacing of 11 kb, possibly doubling the mapping resolution relative to currently available RIL panels. The SNPs were used to construct a genetic map to facilitate QTL analysis. Life history traits, such as lifespan, stress resistance, developmental speed and population growth were measured in different environments. For most traits substantial variation was found, and multiple QTLs could be detected, including novel QTLs not found in previous QTL analysis, for example for lifespan or pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. Taken together, we show that RNA-seq can be used for genotyping, that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates permits analysis of local adaptation and life history trade-offs.

Quantitative trait loci mapping of Meloidogyne incognita and M. hapla resistance in a recombinant inbred line population of soybean

Nematology ◽  
2018 ◽  
Vol 20 (6) ◽  
pp. 525-537
Author(s):  
Chunjie Li ◽  
Jialin Wang ◽  
Jia You ◽  
Xinpeng Wang ◽  
Baohui Liu ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Meloidogyne Incognita ◽  
Qtl Analysis ◽  
Recombinant Inbred Line Population ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Nematode Reproduction ◽  
Root Response

Summary A recombinant inbred line population of soybean (Glycine max) was utilised to identify the quantitative trait loci (QTLs) determining the response to infection by two root-knot nematode species, Meloidogyne incognita and M. hapla, in glasshouse assays. QTL analysis detected seven major and four minor QTLs on seven soybean chromosomes ((Chrs) 1, 7, 8, 10, 14, 18, 20) explaining 6-41% phenotypic variance (PVE) for M. incognita root response and nematode reproduction. Three of the major QTLs, on Chrs 7, 10 and 18, were confirmed in previous reports and two major QTLs on Chrs 14 and 20 were detected for the first time. The QTL analysis with M. hapla provides the first report of a major QTL region mapped on Chr 7, explaining 70-82% PVE in M. hapla root response and nematode reproduction. These novel identified QTLs with flanking markers will be helpful in marker-assisted breeding for nematode resistance in soybean.

scholarly journals Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1690
Author(s):  
Yheni Dwiningsih ◽  
Anuj Kumar ◽  
Julie Thomas ◽  
Charles Ruiz ◽  
Jawaher Alkahtani ◽  
...  
Keyword(s):  
Candidate Genes ◽  
High Throughput ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Genetic Information ◽  
Snp Markers ◽  
Rice Grain ◽  
Grain Length ◽  
Ril Population

Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of “Kaybonnet (KBNT lpa)” and “ZHE733” named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.

scholarly journals Genetic loci mapping for ear axis weight using recombinant inbred line (RIL) population under different nitrogen regimes in maize

2011 ◽  
Vol 10 (42) ◽  
pp. 8255-8259 ◽  
Author(s):  
Zheng Zu Ping ◽  
Liu Xiao Hong ◽  
Wu Xun ◽  
Zhang Yong Si ◽  
He Chuan
Keyword(s):  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Genetic Loci ◽  
Ril Population

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.

scholarly journals RNA-Seq using bulked recombinant inbred line populations uncovers the importance of brassinosteroid for seed longevity after priming treatments

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Naoto Sano ◽  
June-Sik Kim ◽  
Yoshihiko Onda ◽  
Takahito Nomura ◽  
Keiichi Mochida ◽  
...  
Keyword(s):  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Seed Longevity ◽  
Rna Seq
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