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

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.;

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Pathogen-Specific Effects of Quantitative Trait Loci Affecting Clinical Mastitis and Somatic Cell Count in Danish Holstein Cattle

Journal of Dairy Science ◽

10.3168/jds.2007-0583 ◽

2008 ◽

Vol 91 (6) ◽

pp. 2493-2500 ◽

Cited By ~ 19

Author(s):

L.P. Sørensen ◽

B. Guldbrandtsen ◽

J.R. Thomasen ◽

M.S. Lund

Keyword(s):

Quantitative Trait Loci ◽

Somatic Cell ◽

Cell Count ◽

Quantitative Trait ◽

Somatic Cell Count ◽

Clinical Mastitis ◽

Holstein Cattle ◽

Specific Effects ◽

Trait Loci

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Quantitative trait loci affecting clinical mastitis and somatic cell count in dairy cattle

Mammalian Genome ◽

10.1007/s00335001-2081-3 ◽

2001 ◽

Vol 12 (11) ◽

pp. 837-842 ◽

Cited By ~ 70

Author(s):

Helge Klungland ◽

Ayman Sabry ◽

Bjørg Heringstad ◽

Hanne Gro Olsen ◽

Luis Gomez-Raya ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Dairy Cattle ◽

Somatic Cell ◽

Cell Count ◽

Quantitative Trait ◽

Somatic Cell Count ◽

Clinical Mastitis ◽

Trait Loci

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

Canadian Journal of Plant Science ◽

10.4141/cjps10112 ◽

2011 ◽

Vol 91 (1) ◽

pp. 49-55 ◽

Cited By ~ 11

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.

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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

Phytopathology ◽

10.1094/phyto.2004.94.4.370 ◽

2004 ◽

Vol 94 (4) ◽

pp. 370-379 ◽

Cited By ~ 122

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.

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Mapping quantitative trait loci for pre-harvest sprouting resistance in white-grained winter wheat line CA 0431

Crop and Pasture Science ◽

10.1071/cp13102 ◽

2013 ◽

Vol 64 (6) ◽

pp. 573 ◽

Cited By ~ 6

Author(s):

X. L. Miao ◽

Y. J. Zhang ◽

X. C. Xia ◽

Z. H. He ◽

Y. Zhang ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Winter Wheat ◽

Quantitative Trait ◽

Interval Mapping ◽

Field Trials ◽

Economic Losses ◽

Phenotypic Variance ◽

Wheat Line ◽

F2 Population ◽

Trait Loci

Pre-harvest sprouting (PHS) in wheat severely reduces yield and end-use quality, resulting in substantial economic losses. The Chinese winter wheat line CA 0431, with white grain, showed high PHS resistance for many years. To identify quantitative trait loci (QTLs) of PHS resistance in this line, 220 F2 plants and the corresponding F2 : 3 lines derived from a cross between CA 0431 and the PHS-susceptible cultivar Zhongyou 206 were used for PHS testing and QTL analysis. Field trials were conducted in Beijing during the 2010–11 and 2011–12 cropping seasons, and in Anyang during 2011–12. PHS resistance was evaluated by assessing the sprouting responses of intact spikes. In total, 1444 molecular markers were used to screen the parents, and 31 markers with polymorphisms between the resistant and susceptible bulks were used to genotype the entire F2 population. Broad-sense heritability of sprouting rate was 0.71 across environments. Inclusive composite interval mapping identified four QTLs, QPhs.caas-2BL, QPhs.caas-3AS.1, QPhs.caas-3AS.2, and QPhs.caas-3AL, each explaining 2.8–27.7% of the phenotypic variance across environments. The QTLs QPhs.caas-3AS.1, QPhs.caas-3AS.2, and QPhs.caas-3AL were located at similar positions to QTLs reported previously, whereas QPhs.caas-2BL is likely a new QTL flanked by markers Xbarc1042 and Xmag3319. Line CA 0431 and the identified markers can be used in breeding programs targeting improvement of PHS resistance for white-kernel wheat.

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Genome-Wide Association Study in Mexican Holstein Cattle Reveals Novel Quantitative Trait Loci Regions and Confirms Mapped Loci for Resistance to Bovine Tuberculosis

Animals ◽

10.3390/ani9090636 ◽

2019 ◽

Vol 9 (9) ◽

pp. 636 ◽

Cited By ~ 2

Author(s):

Sara González-Ruiz ◽

Maria G. Strillacci ◽

Marina Durán-Aguilar ◽

Germinal J. Cantó-Alarcón ◽

Sara E. Herrera-Rodríguez ◽

...

Keyword(s):

Immune Response ◽

Quantitative Trait Loci ◽

Dairy Cattle ◽

Quantitative Trait ◽

Bovine Tuberculosis ◽

Genome Wide Association ◽

Economic Losses ◽

Genome Wide ◽

Trait Loci ◽

Mycobacterium Spp

Bovine tuberculosis (bTB) is a disease of cattle that represents a risk to public health and causes severe economic losses to the livestock industry. Recently, genetic studies, like genome-wide association studies (GWAS) have greatly improved the investigation of complex diseases identifying thousands of disease-associated genomic variants. Here, we present evidence of genetic variants associated with resistance to TB in Mexican dairy cattle using a case-control approach with a selective DNA pooling experimental design. A total of 154 QTLRs (quantitative trait loci regions) at 10% PFP (proportion of false positives), 42 at 5% PFP and 5 at 1% PFP have been identified, which harbored 172 annotated genes. On BTA13, five new QTLRs were identified in the MACROD2 and KIF16B genes, supporting their involvement in resistance to bTB. Six QTLRs harbor seven annotated genes that have been previously reported as involved in immune response against Mycobacterium spp: BTA (Bos taurus autosome) 1 (CD80), BTA3 (CTSS), BTA 3 (FCGR1A), BTA 23 (HFE), BTA 25 (IL21R), and BTA 29 (ANO9 and SIGIRR). We identified novel QTLRs harboring genes involved in Mycobacterium spp. immune response. This is a first screening for resistance to TB infection on Mexican dairy cattle based on a dense SNP (Single Nucleotide Polymorphism) chip.

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Mapping quantitative trait loci associated with variation in grain dormancy in Australian wheat

Australian Journal of Agricultural Research ◽

10.1071/ar01049 ◽

2001 ◽

Vol 52 (12) ◽

pp. 1257 ◽

Cited By ~ 65

Author(s):

D. J. Mares ◽

K. Mrva

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Preharvest Sprouting ◽

Germination Index ◽

Economic Losses ◽

Doubled Haploid Population ◽

Grain Dormancy ◽

Grain Handling ◽

Trait Loci ◽

Haploid Population

Preharvest sprouting is a problem in many regions of the world, resulting in downgrading of quality, substantial economic losses to wheat growers, and difficulties for grain handling and marketing agencies. Improvements in tolerance from the introduction of better grain dormancy at, or near, harvest-ripeness would be expected to have a significant impact on the incidence and severity of sprouting. Intermediate levels of dormancy in older Australian wheats, such as Halberd, and a small number of current cultivars could be used in the short term while more extreme dormancy is being introgressed into locally adapted germplasm. A doubled haploid population derived from Cranbrook (extremely non-dormant, very susceptible to sprouting) x Halberd (intermediate dormancy, moderately tolerant to preharvest sprouting) was grown in replicated experiments and ripe grain harvested for assessment of dormancy, measured as a germination index. Consistent differences were observed between the parents in both experiments. For the bulk of the progeny, the germination index fell within a range defined by Cranbrook at the upper and Halberd at the lower end. Significant quantitative trait loci, all contributed by the very susceptible parent, that explained 11%, 9%, and 9% of the phenotypic variation were identified on chromosome arms 2AL, 2DL, and 4AL, respectively. These QTLs offer the opportunity to develop molecular markers for grain dormancy and to develop a better understanding of the mechanisms involved in this trait.

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A comparison between methods for linkage disequilibrium fine mapping of quantitative trait loci

Genetics Research ◽

10.1017/s0016672303006554 ◽

2004 ◽

Vol 83 (1) ◽

pp. 41-47 ◽

Cited By ~ 8

Author(s):

JIHAD M. ABDALLAH ◽

BRIGITTE MANGIN ◽

BRUNO GOFFINET ◽

CHRISTINE CIERCO-AYROLLES ◽

MIGUEL PÉREZ-ENCISO

Keyword(s):

Linkage Disequilibrium ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Simulated Data ◽

Likelihood Method ◽

Trait Loci ◽

Single Marker ◽

Linkage Disequilibrium Information ◽

Marker Regression ◽

Trait Locus

We present a maximum likelihood method for mapping quantitative trait loci that uses linkage disequilibrium information from single and multiple markers. We made paired comparisons between analyses using a single marker, two markers and six markers. We also compared the method to single marker regression analysis under several scenarios using simulated data. In general, our method outperformed regression (smaller mean square error and confidence intervals of location estimate) for quantitative trait loci with dominance effects. In addition, the method provides estimates of the frequency and additive and dominance effects of the quantitative trait locus.

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