Quantitative trait loci analysis of seed coat color components for selective breeding in chickpea (Cicer arietinum L.)

2011 ◽  
Vol 91 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Shanoor Hossain ◽  
Joe Panozzo ◽  
Chris Pittock ◽  
Rebecca Ford
Keyword(s):  
Quantitative Trait Loci ◽  
Seed Coat ◽  
Quantitative Trait ◽  
Selective Breeding ◽  
Coat Color ◽  
Seed Coat Color ◽  
Breeding Programs ◽  
Cicer Arietinum L ◽  
Trait Loci ◽  
Color Components

Hossain, S., Panozzo, J. F., Pittock, C. and Ford, R. 2011. Quantitative trait loci analysis of seed coat color components for selective breeding in chickpea (Cicer arietinumL.). Can. J. Plant Sci. 91: 49–55. Chickpea (Cicer arietinum L.) is an annual grain legume, grown worldwide for human consumption with the potential to attract premium prices in markets such as India, Bangladesh and southern Asia. The ability to accurately select for seed coat color, an important export quality trait, would greatly benefit chickpea breeding programs. In order to determine the major genomic loci governing the color trait, the color components of CIE L* (luminance), CIE a* (red/green color) and CIE b* (blue/yellow color), C* (chroma or saturation of the color) and h° (hue or purity of the color) were mapped, and associated molecular markers were identified. A linkage map was constructed with 80 SSR markers distributed over 10 linkage groups at an average marker density of 2.8 cM. Two major quantitative trait loci (QTL), which accounted for up to 36 and 49% of the genetic variance and several smaller genetic effects were determined to govern the color components. These were consistent across two differing environments. Once validated, the markers that are close to and flanking these QTL and significantly associated with the minor gene effects will be useful in future color selective breeding programs.

scholarly journals Quantitative Trait Loci (QTL) Analysis Reveals Both Broad-Spectrum and Isolate-Specific QTL for Scab Resistance in an Apple Progeny Challenged with Eight Isolates of Venturia inaequalis

2004 ◽  
Vol 94 (4) ◽  
pp. 370-379 ◽  
Author(s):  
F. Calenge ◽  
A. Faure ◽  
M. Goerre ◽  
C. Gebhardt ◽  
W. E. Van de Weg ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Quantitative Trait ◽  
Venturia Inaequalis ◽  
Scab Resistance ◽  
Breeding Programs ◽  
Apple Breeding ◽  
Trait Loci ◽  
New Races

The major scab resistance gene Vf, extensively used in apple breeding programs, was recently overcome by the new races 6 and 7 of the fungal pathogen Venturia inaequalis. New, more durable, scab resistance genes are needed in apple breeding programs. F1 progeny derived from the cross between partially resistant apple cv. Discovery and apple hybrid ‘TN10-8’ were inoculated in the greenhouse with eight isolates of V. inaequalis, including isolates able to overcome Vf. One major resistance gene, Vg, and seven quantitative trait loci (QTL) were identified for resistance to these isolates. Three QTL on linkage group (LG)12, LG13, and LG15 were clearly isolate-specific. Another QTL on LG5 was detected with two isolates. Three QTL on LG1, LG2, and LG17 were identified with most isolates tested, but not with every isolate. The QTL on LG2 displayed alleles conferring different specificities. This QTL co-localized with the major scab resistance genes Vr and Vh8, whereas the QTL on LG1 colocalized with Vf. These results contribute to a better understanding of the genetic basis of the V. inaequalis-Malus × domestica interaction.

scholarly journals The genomics of growth and blue spots in a cultured population of Australasian snapper Chrysophrys auratus

2021 ◽  
Author(s):  
◽  
David T. Ashton
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Quantitative Trait ◽  
Selective Breeding ◽  
Genomic Research ◽  
Linkage Groups ◽  
Teleost Species ◽  
Genome Data ◽  
Wide Range ◽  
Trait Loci

<p>Characterizing the genome and understanding how it influences phenotypic variation is a central goal for studies on evolution. The findings of genomic research are applicable to a wide range of human endeavours, including predicting disease risk, supporting selective breeding programmes, and understanding adaptive variation in natural populations. One industry that could particularly benefit from this knowledge is Aquaculture. In recent years, aquaculture production has been increasing to offset the production limits of wild fisheries. Genomics can be used in aquaculture to quantify variation of captive populations, reconstruct pedigrees, and improve the gains from selective breeding programs. The overall goal of this thesis research was to generate a genome-wide genotyping dataset and investigated several key traits for Australasian snapper (Chrysophrys auratus or Pagrus auratus). The findings will be used to establish one of the first genomics-informed New Zealand aquaculture programmes and provide a better understanding of the genotype-phenotype relationships in this teleost species.  The first two chapters of this thesis provide a review of the literature and establish the background information and context for the research in subsequent data chapters. A brief overview of genomics, fisheries and aquaculture, and the intersection of these two fields are provided in the Chapter 1. An in-depth quantitative review of 146 Quantitative Trait Loci (QTL) studies in teleost fish was then carried out in Chapter 2.  Chapter 3 provides details about the study population and the collection of genotyping data. Genotyping-By-Sequencing (GBS) was used to generate 11K Single Nucleotide Polymorphism (SNP) markers for individuals in the three generation pedigree. Together with phenotypic data the genotyping was used to reconstruct the pedigree, measure inbreeding, and estimate heritability for a range of traits. Parents were identified for 93% of the offspring and successful pedigree reconstruction indicated highly uneven contributions of each parent to the subsequent generations. The average inbreeding level did not change between generations, but significantly different inbreeding levels were observed between offspring from the two founding cohorts and as a result full and half sibling crosses within the group spawning teleost species. Heritability was estimated for a range of traits using both a pedigree relatedness matrix and a genomic relatedness matrix.  Chapter 4, uses the genotyping and phenotyping data to generate a linkage map and carry out a scan for quantitative trait loci (QTLs) associated with growth rate. The linkage map reported in this thesis is one of the highest density maps for any Sparidae species at the time of writing. It contained 24 linkage groups, which represent the 24 snapper chromosomes. Growth QTLs were found on three linkage groups and a scan of available genome data identified three candidate growth genes nearby on the linkage groups.  Chapter 5, uses the genotyping data and images collected during the study to characterize snappers blue spots and search for QTLs associated with spot numbers. QTLs were found on 12 of the 24 linkage groups, of which one was consistent between two QTL methods applied. A scan of available genome data identified the tyrosinase gene in the middle of the putative QTL region, which is a causal gene for iridophore cell numbers that form blue spots in other fish species.  Chapter 6, discuss the implications, future directions, and application of this research to the snapper breeding programme.</p>

Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.)

2005 ◽  
Vol 111 (2) ◽  
pp. 185-195 ◽  
Author(s):  
S. Abbo ◽  
C. Molina ◽  
R. Jungmann ◽  
M. A. Grusak ◽  
Z. Berkovitch ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Cicer Arietinum ◽  
Quantitative Trait ◽  
Carotenoid Concentration ◽  
Cicer Arietinum L ◽  
Trait Loci

scholarly journals Quantitative trait loci for udder conformation and other udder traits in Finnish Ayrshire cattle

2008 ◽  
Vol 16 (2) ◽  
pp. 170
Author(s):  
N.F. SCHULMAN ◽  
S.M. VIITALA ◽  
J.H. VILKKI
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Somatic Cell Count ◽  
Dairy Farms ◽  
Clinical Mastitis ◽  
Economic Losses ◽  
Breeding Programs ◽  
Trait Loci ◽  
Marker Regression ◽  
Body Stature

Udder traits are important due to their correlation with clinical mastitis which causes major economic losses to the dairy farms. Chromosomal areas associated with udder conformation traits, milking speed and leakage could be used in breeding programs to improve both udder traits and mastitis resistance. Quantitative trait loci (QTL) mapping for udder traits was carried out on bovine chromosomes (BTA) 9, 11, 14, 18, 20, 23, and 29, where earlier studies have indicated QTL for mastitis. A granddaughter design with 12 Ayrshire sire families and 360 sons was used. The sires and sons were typed for 35 markers. The traits analysed were udder depth, fore udder attachment, central ligament, distance from udder to floor, body stature, fore teat length, udder balance, rear udder height, milking speed, and leakage. Associations between markers and traits were analysed with multiple marker regression. Five genome-wise significant QTL were detected: stature on BTA14 and 23, udder balance on BTA23, rear udder height on BTA11, and central ligament on BTA23. On BTA11 and 14 the suggested QTL positions for udder traits are at the same position as previously detected QTL for mastitis and somatic cell count.;

scholarly journals The genomics of growth and blue spots in a cultured population of Australasian snapper Chrysophrys auratus

2021 ◽  
Author(s):  
◽  
David T. Ashton
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Quantitative Trait ◽  
Selective Breeding ◽  
Genomic Research ◽  
Linkage Groups ◽  
Teleost Species ◽  
Genome Data ◽  
Wide Range ◽  
Trait Loci

<p>Characterizing the genome and understanding how it influences phenotypic variation is a central goal for studies on evolution. The findings of genomic research are applicable to a wide range of human endeavours, including predicting disease risk, supporting selective breeding programmes, and understanding adaptive variation in natural populations. One industry that could particularly benefit from this knowledge is Aquaculture. In recent years, aquaculture production has been increasing to offset the production limits of wild fisheries. Genomics can be used in aquaculture to quantify variation of captive populations, reconstruct pedigrees, and improve the gains from selective breeding programs. The overall goal of this thesis research was to generate a genome-wide genotyping dataset and investigated several key traits for Australasian snapper (Chrysophrys auratus or Pagrus auratus). The findings will be used to establish one of the first genomics-informed New Zealand aquaculture programmes and provide a better understanding of the genotype-phenotype relationships in this teleost species.  The first two chapters of this thesis provide a review of the literature and establish the background information and context for the research in subsequent data chapters. A brief overview of genomics, fisheries and aquaculture, and the intersection of these two fields are provided in the Chapter 1. An in-depth quantitative review of 146 Quantitative Trait Loci (QTL) studies in teleost fish was then carried out in Chapter 2.  Chapter 3 provides details about the study population and the collection of genotyping data. Genotyping-By-Sequencing (GBS) was used to generate 11K Single Nucleotide Polymorphism (SNP) markers for individuals in the three generation pedigree. Together with phenotypic data the genotyping was used to reconstruct the pedigree, measure inbreeding, and estimate heritability for a range of traits. Parents were identified for 93% of the offspring and successful pedigree reconstruction indicated highly uneven contributions of each parent to the subsequent generations. The average inbreeding level did not change between generations, but significantly different inbreeding levels were observed between offspring from the two founding cohorts and as a result full and half sibling crosses within the group spawning teleost species. Heritability was estimated for a range of traits using both a pedigree relatedness matrix and a genomic relatedness matrix.  Chapter 4, uses the genotyping and phenotyping data to generate a linkage map and carry out a scan for quantitative trait loci (QTLs) associated with growth rate. The linkage map reported in this thesis is one of the highest density maps for any Sparidae species at the time of writing. It contained 24 linkage groups, which represent the 24 snapper chromosomes. Growth QTLs were found on three linkage groups and a scan of available genome data identified three candidate growth genes nearby on the linkage groups.  Chapter 5, uses the genotyping data and images collected during the study to characterize snappers blue spots and search for QTLs associated with spot numbers. QTLs were found on 12 of the 24 linkage groups, of which one was consistent between two QTL methods applied. A scan of available genome data identified the tyrosinase gene in the middle of the putative QTL region, which is a causal gene for iridophore cell numbers that form blue spots in other fish species.  Chapter 6, discuss the implications, future directions, and application of this research to the snapper breeding programme.</p>

scholarly journals Linkage mapping and quantitative trait loci analysis of sweetness and other fruit quality traits in papaya

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Usana Nantawan ◽  
Chutchamas Kanchana-udomkan ◽  
Ido Bar ◽  
Rebecca Ford
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Fruit Quality ◽  
Quantitative Trait ◽  
Selective Breeding ◽  
Fruit Weight ◽  
Phenotypic Variance ◽  
Quality Traits ◽  
Fruit Quality Traits ◽  
Trait Loci

Abstract Background The identification and characterisation of quantitative trait loci (QTL) is an important step towards identifying functional sequences underpinning important crop traits and for developing accurate markers for selective breeding strategies. In this study, a genotyping-by-sequencing (GBS) approach detected QTL conditioning desirable fruit quality traits in papaya. Results For this, a linkage map was constructed comprising 219 single nucleotide polymorphism (SNP) loci across 10 linkage groups and covering 509 centiMorgan (cM). In total, 21 QTLs were identified for seven key fruit quality traits, including flesh sweetness, fruit weight, fruit length, fruit width skin freckle, flesh thickness and fruit firmness. Several QTL for flesh sweetness, fruit weight, length, width and firmness were stable across harvest years and individually explained up to 19.8% of the phenotypic variance of a particular trait. Where possible, candidate genes were proposed and explored further for their application to marker-assisted breeding. Conclusions This study has extended knowledge on the inheritance and genetic control for key papaya physiological and fruit quality traits. Candidate genes together with associated SNP markers represent a valuable resource for the future of strategic selective breeding of elite Australian papaya cultivars.

scholarly journals Genetic Analysis and Molecular Mapping of Quantitative Trait Loci in Common Bean Against Pythium ultimum

2010 ◽  
Vol 100 (12) ◽  
pp. 1315-1320 ◽  
Author(s):  
Ana Campa ◽  
Elena Pérez-Vega ◽  
Aida Pascual ◽  
Juan José Ferreira
Keyword(s):  
Quantitative Trait Loci ◽  
Common Bean ◽  
Seed Coat ◽  
Quantitative Trait ◽  
Molecular Mapping ◽  
Recombinant Inbred Lines ◽  
Pythium Ultimum ◽  
Seedling Vigor ◽  
Emergence Rate ◽  
Trait Loci

Pythium ultimum is a soil pathogen that can cause seed decay and damage to roots in common bean. In this study, the response of a set of 40 common bean genotypes to P. ultimum and inheritance of the resistance in the 92 F7 recombinant inbred lines (RIL) developed from a cross between Xana and Cornell 49242 was investigated by using emergence rate and seedling vigor. Emergence of the 40 genotypes showed a significant association between white seed coat and response to this pathogen. Among these, 11 common bean genotypes, all with colored seeds, exhibited a high percentage of emergence and seedling vigor not significantly different (P > 0.05) to noninoculated plants. Response of the RIL population revealed both qualitative and quantitative modes of inheritance. A major gene (Py-1) controlling the emergence rate was mapped in the region of the gene P, a basic color gene involved in control of seed coat color, located on LG 7. Using the RIL subpopulation with colored seeds, a significant quantitative trait loci (QTL) associated with the emergence rate (ER3XC) and another with seedling vigor (SV6XC) were identified on the LG 3 and 6, respectively. QTL SV6XC was mapped in the region of the gene V, another gene involved the genetic control of color. QTLs associated with seed traits were mapped in the same relative position as regions involved in responses to P. ultimum suggesting the possible implication of avoidance mechanisms in the response to this pathogen.

scholarly journals Quantitative Trait Loci Associated with Sex Expression in an Inter-subspecific Watermelon Population

2013 ◽  
Vol 138 (2) ◽  
pp. 125-130 ◽  
Author(s):  
Jason Prothro ◽  
Hussein Abdel-Haleem ◽  
Eleni Bachlava ◽  
Victoria White ◽  
Steven Knapp ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Citrullus Lanatus ◽  
Draft Genome ◽  
Sex Expression ◽  
Breeding Programs ◽  
Trait Loci ◽  
Important Trait ◽  
Percent Female

Sex expression is an important trait in watermelon (Citrullus lanatus), in which monoecious, andromonoecious, and trimonoecious forms are present. The andromonoecious trait is highly undesirable in watermelon breeding programs because it would require emasculation during hybrid development. In contrast to other cucurbits such as melon (Cucumis melo) and cucumber (Cucumis sativus) in which the genes involved in sex expression are well described and have been cloned, only the inheritance of the a gene associated with the andromonoecious trait has been described in watermelon. We used an intersubspecific C. lanatus var. lanatus × C. lanatus var. citroides F2 population to map quantitative trait loci (QTL) associated with percent male (%M), percent female (%F), percent hermaphrodite (%HM), and percent female of pistillate [%F/P (female + hermaphrodite)] flowers. Four chromosomal regions were identified that were associated with sex expression in watermelon. Major QTL for %F, %HM, and %F/P were colocalized on linkage group 11A and explained 31.3% to 37.7% of the phenotypic variation observed for the three traits. These QTL are suggested to be the location of the a gene in watermelon. Markers linked to two of the four QTL identified were located within 1 Mb of a 1-aminocyclopropane-1-carboxylic acid synthase (ACS) gene on the watermelon draft genome. ACS genes play a key role in sex expression in melon and cucumber and these genes are therefore candidate genes for further studies to elucidate this trait in another economically important cucurbit crop. The QTL and candidate genes identified in the present study lay the foundation for marker-assisted selection for sex expression traits in watermelon.

Sign in / Sign up

Export Citation Format

Share Document