scholarly journals Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 735
Author(s):  
Mohammad Ibrahim Haqani ◽  
Shigeru Nomura ◽  
Michiharu Nakano ◽  
Tatsuhiko Goto ◽  
Atsushi J. Nagano ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Dna Sequencing ◽  
Japanese Quail ◽  
Quantitative Trait ◽  
Restriction Site ◽  
Snp Markers ◽  
Egg Weight ◽  
Second Stage ◽  
Trait Loci ◽  
Egg Shell

This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F2 females were produced by full-sib mating of F1 birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

scholarly journals Mapping of Quantitative Trait Loci for Growth and Carcass-Related Traits in Chickens Using a Restriction-Site Associated DNA Sequencing Method

2019 ◽  
Vol 56 (3) ◽  
pp. 166-176
Author(s):  
Takashi Ono ◽  
Ken Ohara ◽  
Akira Ishikawa ◽  
Tomomi Kouguchi ◽  
Atsushi J. Nagano ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Dna Sequencing ◽  
Quantitative Trait ◽  
Restriction Site ◽  
Sequencing Method ◽  
Trait Loci

scholarly journals Identification of quantitative trait loci for flowering time by a combination of restriction site–associated DNA sequencing and bulked segregant analysis in soybean

2017 ◽  
Vol 67 (3) ◽  
pp. 277-285 ◽  
Author(s):  
Satoshi Watanabe ◽  
Chikaharu Tsukamoto ◽  
Tatsuki Oshita ◽  
Tetsuya Yamada ◽  
Toyoaki Anai ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Dna Sequencing ◽  
Flowering Time ◽  
Quantitative Trait ◽  
Restriction Site ◽  
Bulked Segregant Analysis ◽  
Trait Loci

scholarly journals A Fine mapping quantitative trait loci that underlie resistance to soybean sudden death syndrome using NILs and SNPs.

2018 ◽  
pp. 583-591
Author(s):  
Yi Chen Lee ◽  
M Javed Iqbal ◽  
Victor N Njiti ◽  
Stella Kantartzi ◽  
David A. Lightfoot
Keyword(s):  
Quantitative Trait Loci ◽  
Sudden Death ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Soybean Cyst Nematode ◽  
Snp Markers ◽  
Sudden Death Syndrome ◽  
Isogenic Line ◽  
Trait Loci ◽  
Glycine Max L

Soybean (Glycine max (L.) Merr.) cultivars differ in their resistance to sudden death syndrome (SDS), caused by Fusarium virguliforme. Breeding for improving SDS response has been challenging, due to interactions among the 18-42 known resistance loci. Four quantitative trait loci (QTL) for resistance to SDS (cqRfs–cqRfs3) were clustered within 20 cM of the rhg1 locus underlying resistance to soybean cyst nematode (SCN) on Chromosome (Chr.) 18. Another locus on Chr. 20 (cqRfs5) was reported to interact with this cluster. The aims here were to compare the inheritance of resistance to SDS in a near isogenic line (NIL) population that was fixed for resistance to SCN but segregated at two of the four loci (cqRfs1 and cqRfs) for SDS resistance; to examine the interaction with the locus on Chr. 20; and to identify candidate genes underlying QTL. Used were; a NIL population derived from residual heterozygosity in an F5:7 recombinant inbred line EF60 (lines 1-38); SDS response data from two locations and years; four segregating microsatellite and 1,500 SNP markers. Polymorphic regions were found from 2,788 Kbp to 8,938 Kbp on Chr. 18 and 33,100 Kbp to 34,943 Kbp on Chr. 20 that were significantly (0.005 < P > 0.0001) associated with resistance to SDS. The QTL fine maps suggested that the two loci on Chr. 18 were three loci (cqRfs1, cqRfs, and cqRfs19). Candidate genes were inferred.  An epistatic interaction was inferred between Chr. 18 and Chr. 20 loci. Therefore, SDS resistance QTL were both complex and interacting.

Whole genome fine mapping of quantitative trait loci for ultrasound and carcass merit traits in beef cattle

2011 ◽  
Vol 91 (1) ◽  
pp. 61-73 ◽  
Author(s):  
Sungael Nalaila ◽  
Paul Stothard ◽  
Stephen Moore ◽  
Zhiquan Wang ◽  
Changxi Li
Keyword(s):  
Quantitative Trait Loci ◽  
Beef Cattle ◽  
Fine Mapping ◽  
Quantitative Trait ◽  
Snp Markers ◽  
Whole Genome ◽  
Association Analyses ◽  
University Of Alberta ◽  
Trait Loci ◽  
Carcass Merit

Nalaila, S. M., Stothard, P., Moore, S. S., Wang, Z. and Li, C. 2011. Whole genome fine mapping of quantitative trait loci for ultrasound and carcass merit traits in beef cattle. Can. J. Anim. Sci. 91: 61–73. Quantitative trait loci (QTL) mapped to large chromosomal regions have limited utility as DNA markers for marker-assisted selection (MAS) and are less informative as a reference for the identification of the underlying causative quantitative trait nucleotides (QTN). The objective of this study was to conduct a whole genome fine mapping of QTL for ultrasound and carcass merit traits in beef cattle using a greater density of single nucleotide polymorphism (SNP) markers, and to identify SNP markers within the QTL regions that are associated with the traits. A total of 418 steers from 28 sires were used in this study with nine ultrasound and seven carcass merit traits that were collected as part of a feedlot trial conducted from 2003 to 2005 at the University of Alberta Kinsella ranch. Sires and their progeny were genotyped for a total of 4592 SNP markers distributed across all 29 bovine autosomes (BTA). Across-family analyses detected 12 QTL for five ultrasound traits on nine chromosomes and 18 QTL for six carcass merit traits on 10 chromosomes (P<0.05). Within-family analyses identified 78 significant QTL for nine ultrasound and seven carcass merit traits (P<0.01). The use of a denser panel of SNP markers allowed fine mapping of QTL to smaller chromosomal regions ranging from 0.6 to 11 cM compared with relatively larger QTL regions of 4 to 24 cM reported in previous studies. Furthermore, single SNP marker association analyses identified 22 SNPs that were significantly associated with three ultrasound and four carcass merit traits under 12 QTL regions (P<0.05). These identified SNP markers significantly associated with the traits under the fine mapped QTL regions provide genomic tools for potential application of MAS and a reference to assist with the identification of QTN causing variations in ultrasound and carcass merit traits in beef cattle.

scholarly journals High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing

2021 ◽  
pp. PHYTO-12-19-048
Author(s):  
Kai Su ◽  
Yinshan Guo ◽  
Weihao Zhong ◽  
Hong Lin ◽  
Zhendong Liu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Dna Sequencing ◽  
Quantitative Trait ◽  
Restriction Site ◽  
Genetic Distances ◽  
Snp Markers ◽  
High Density ◽  
White Rot ◽  
Phenotypic Variance ◽  
Trait Locus

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca ‘Zhuosexiang’) and white rot-susceptible cultivar (V. vinifera ‘Victoria’). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.

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