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https://www.readbyqxmd.com/read/29785919/genomic-selection-in-dairy-cattle-simulated-populations
#1
Leonardo de Oliveira Seno, Diego Gomes Freire Guidolin, Rusbel Raul Aspilcueta-Borquis, Guilherme Batista do Nascimento, Thiago Bruno Ribeiro da Silva, Henrique Nunes de Oliveira, Danísio Prado Munari
Genomic selection is arguably the most promising tool for improving genetic gain in domestic animals to emerge in the last few decades, but is an expensive process. The aim of this study was to evaluate the economic impact related to the implementation of genomic selection in a simulated dairy cattle population. The software QMSim was used to simulate genomic and phenotypic data. The simulated genome contained 30 chromosomes with 100 cm each, 1666 SNPs markers equally spread and 266 QTLs randomly designated for each chromosome...
May 2018: Journal of Dairy Research
https://www.readbyqxmd.com/read/29785904/identification-of-an-immune-modulation-locus-utilising-a-bovine-mammary-gland-infection-challenge-model
#2
Mathew D Littlejohn, Sally-Anne Turner, Caroline G Walker, Sarah D Berry, Kathryn Tiplady, Ric G Sherlock, Greg Sutherland, Simon Swift, Dorian Garrick, S Jane Lacy-Hulbert, Scott McDougall, Richard J Spelman, Russell G Snell, J Eric Hillerton
Inflammation of the mammary gland following bacterial infection, commonly known as mastitis, affects all mammalian species. Although the aetiology and epidemiology of mastitis in the dairy cow are well described, the genetic factors mediating resistance to mammary gland infection are not well known, due in part to the difficulty in obtaining robust phenotypic information from sufficiently large numbers of individuals. To address this problem, an experimental mammary gland infection experiment was undertaken, using a Friesian-Jersey cross breed F2 herd...
May 2018: Journal of Dairy Research
https://www.readbyqxmd.com/read/29785398/marker-assisted-introgression-of-saltol-qtl-enhances-seedling-stage-salt-tolerance-in-the-rice-variety-pusa-basmati-1
#3
Vivek Kumar Singh, Brahma Deo Singh, Amit Kumar, Sadhna Maurya, Subbaiyan Gopala Krishnan, Kunnummal Kurungara Vinod, Madan Pal Singh, Ranjith Kumar Ellur, Prolay Kumar Bhowmick, Ashok Kumar Singh
Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol . A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29783939/a-genome-wide-association-study-reveals-novel-genomic-regions-and-positional-candidate-genes-for-fat-deposition-in-broiler-chickens
#4
Gabriel Costa Monteiro Moreira, Clarissa Boschiero, Aline Silva Mello Cesar, James M Reecy, Thaís Fernanda Godoy, Priscila Anchieta Trevisoli, Maurício E Cantão, Mônica Corrêa Ledur, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Ana Silvia Alves Meira Tavares Moura, Dorian Garrick, Luiz Lehmann Coutinho
BACKGROUND: Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken's carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29780395/genetic-analysis-of-fusarium-head-blight-resistance-in-cimmyt-bread-wheat-line-c615-using-traditional-and-conditional-qtl-mapping
#5
Xin Yi, Jingye Cheng, Zhengning Jiang, Wenjing Hu, Tongde Bie, Derong Gao, Dongsheng Li, Ronglin Wu, Yuling Li, Shulin Chen, Xiaoming Cheng, Jian Liu, Yong Zhang, Shunhe Cheng
Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29776327/utility-of-whole-genome-sequence-data-for-across-breed-genomic-prediction
#6
Biaty Raymond, Aniek C Bouwman, Chris Schrooten, Jeanine Houwing-Duistermaat, Roel F Veerkamp
BACKGROUND: Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. METHODS: Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands...
May 18, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29775500/endosperm-sugar-accumulation-caused-by-mutation-of-phs8-isa1-leads-to-pre-harvest-sprouting-in-rice
#7
Lin Du, Fan Xu, Jun Fang, Shaopei Gao, Jiuyou Tang, Shuang Fang, Hongru Wang, Hongning Tong, Fengxia Zhang, Jinfang Chu, Guodong Wang, Chengcai Chu
Pre-harvest sprouting (PHS) is an unfavorable trait in cereal crops which could seriously decrease grain yield and quality. Although some PHS-associated quantitative trait loci (QTL) or genes in cereals have been reported, the molecular mechanism underlying PHS remains largely elusive. Here, we characterized a rice mutant, phs8, which exhibits PHS phenotype accompanied by sugary endosperm. Map-based cloning revealed that PHS8 encodes a starch debranching enzyme named isoamylase1. Mutation in PHS8 resulted in the phytoglycogen breakdown and sugar accumulation in the endosperm...
May 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29773962/discovery-and-validation-of-genomic-regions-associated-with-resistance-to-maize-lethal-necrosis-in-four-biparental-populations
#8
Manje Gowda, Yoseph Beyene, Dan Makumbi, Kassa Semagn, Michael S Olsen, Jumbo M Bright, Biswanath Das, Stephen Mugo, L M Suresh, Boddupalli M Prasanna
In sub-Saharan Africa, maize is the key determinant of food security for smallholder farmers. The sudden outbreak of maize lethal necrosis (MLN) disease is seriously threatening the maize production in the region. Understanding the genetic basis of MLN resistance is crucial. In this study, we used four biparental populations applied linkage mapping and joint linkage mapping approaches to identify and validate the MLN resistance-associated genomic regions. All populations were genotyped with low to high density markers and phenotyped in multiple environments against MLN under artificial inoculation...
2018: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/29770990/pool-based-genome-wide-association-study-identified-novel-candidate-regions-on-bta9-and-14-for-oleic-acid-percentage-in-japanese-black-cattle
#9
Fuki Kawaguchi, Hiroto Kigoshi, Ayaka Nakajima, Yuta Matsumoto, Yoshinobu Uemoto, Moriyuki Fukushima, Emi Yoshida, Eiji Iwamoto, Takayuki Akiyama, Namiko Kohama, Eiji Kobayashi, Takeshi Honda, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki
Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1...
May 17, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/29767798/genome-wide-association-of-yield-traits-in-a-nested-association-mapping-population-of-barley-reveals-new-gene-diversity-for-future-breeding
#10
Rajiv Sharma, Fulvia Draicchio, Hazel Bull, Paul Herzig, Andreas Maurer, Klaus Pillen, William T B Thomas, Andrew J Flavell
To explore wild barley as a source of useful alleles for yield improvement in breeding we have carried out a genome-wide association scan using the nested association mapping population HEB-25, which contains 25 diverse exotic barley genomes superimposed on a ca 70% genetic background of cultivated barley. 1420 HEB-25 lines were trialled for nine yield-related grain traits for two years in Germany and Scotland, with varying N-fertilizer application. The phenotypic data were related to genotype scores for 5,398 gene-based SNP markers...
May 15, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29767279/identification-and-validation-of-qtl-for-grain-yield-and-plant-water-status-under-contrasting-water-treatments-in-fall-sown-spring-wheats
#11
Junli Zhang, Shiferaw Abate Gizaw, Eligio Bossolini, Joshua Hegarty, Tyson Howell, Arron H Carter, Eduard Akhunov, Jorge Dubcovsky
Chromosome regions affecting grain yield, grain yield components and plant water status were identified and validated in fall-sown spring wheats grown under full and limited irrigation. Increases in wheat production are required to feed a growing human population. To understand the genetic basis of grain yield in fall-sown spring wheats, we performed a genome-wide association study (GWAS) including 262 photoperiod-insensitive spring wheat accessions grown under full and limited irrigation treatments. Analysis of molecular variance showed that 4...
May 16, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29766218/qtl-mapping-and-epistatic-interaction-analysis-of-field-resistance-to-sudden-death-syndrome-fusarium-virguliforme-in-soybean
#12
Ruijuan Tan, Bradley Serven, Paul J Collins, Zhongnan Zhang, Zixiang Wen, John F Boyse, Cuihua Gu, Martin I Chilvers, Brian W Diers, Dechun Wang
Two interactive quantitative trait loci (QTLs) controlled the field resistance to sudden death syndrome (SDS) in soybean. The interaction between them was confirmed. Sudden death syndrome (SDS), caused by Fusarium virguliforme, is a major disease of soybean [Glycine max (L.) Merr.] in the United States. Breeding for soybean resistance to SDS is the most cost-effective method to manage the disease. The objective of this study was to identify and characterize quantitative trait loci (QTLs) underlying field resistance to SDS in a recombinant inbred line population from the cross GD2422 × LD01-5907...
May 15, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29764961/genome-wide-search-for-quantitative-trait-loci-controlling-important-plant-and-flower-traits-in-petunia-using-an-interspecific-recombinant-inbred-population-of-petunia-axillaris-and-petunia-exserta
#13
Zhe Cao, Yufang Guo, Qian Yang, Yanhong He, Mohammed Fetouh, Ryan M Warner, Zhanao Deng
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia...
May 15, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29761461/bovine-genome-database-tools-for-mining-the-bos-taurus-genome
#14
Darren E Hagen, Deepak R Unni, Aditi Tayal, Gregory W Burns, Christine G Elsik
The Bovine Genome Database (BGD; http://bovinegenome.org ) is a web-accessible resource that supports bovine genomics research by providing genome annotation and data mining tools. BovineMine is a tool within BGD that integrates BGD data, including the genome, genes, precomputed gene expression levels and variant consequences, with external data sources that include quantitative trait loci (QTL), orthologues, Gene Ontology, gene interactions, and pathways. BovineMine enables researchers without programming skills to create custom integrated datasets for use in downstream analyses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29760203/a-dense-linkage-map-of-lake-victoria-cichlids-improved-the-pundamilia-genome-assembly-and-revealed-a-major-qtl-for-sex-determination
#15
Philine G D Feulner, Julia Schwarzer, Marcel P Haesler, Joana I Meier, Ole Seehausen
Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids ( Pundamilia pundamilia and P. sp. 'red head'). The SNP markers were distributed on 22 linkage groups and the total map size was 1,594 cM with an average marker distance of 1...
May 14, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29760201/a-high-resolution-genetic-map-for-the-laboratory-rat
#16
John Littrell, Shirng-Wern Tsaih, Amelie Baud, Pasi Rastas, Leah Solberg-Woods, Michael J Flister
An accurate and high-resolution genetic map is critical for mapping complex traits, yet the resolution of the current rat genetic map is far lower than human and mouse, and has not been updated since the original Jensen-Seaman map in 2004. For the first time, we have refined the rat genetic map to sub-centimorgan (cM) resolution (<0.02 cM) by using 95,769 genetic markers and 870 informative meiosis from a cohort of 528 heterogeneous stock (HS) rats. Global recombination rates in the revised sex-averaged map (0...
May 14, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29757987/genomic-regions-analysis-of-seedling-root-traits-and-their-regulation-in-responses-to-phosphorus-deficiency-tolerance-in-cssl-population-of-elite-super-hybrid-rice
#17
Galal Bakr Anis, Yingxin Zhang, Huimin Wang, Zihe Li, Weixun Wu, Lianping Sun, Aamir Riaz, Liyong Cao, Shihua Cheng
Phosphorus (P) is the essential macro-element supporting rice productivity. Quantitative trait loci (QTL) underlying related traits at the seedling stage under two different phosphorus levels was investigated in rice using a population of 76 Chromosomal Sequence Substitution Lines (CSSLs) derived from a cross between the maintainer variety XieqingzaoB (P stress tolerant) and the restorer variety Zhonghui9308 (P stress sensitive); the parents of super hybrid rice Xieyou9308. A genetic linkage map with 120 DNA marker loci was constructed...
May 14, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29754326/acid-phosphatase-gene-gmhad1-linked-to-low-phosphorus-tolerance-in-soybean-through-fine-mapping
#18
Zhandong Cai, Yanbo Cheng, Peiqi Xian, Qibin Ma, Ke Wen, Qiuju Xia, Gengyun Zhang, Hai Nian
Map-based cloning identified GmHAD1, a gene which encodes a HAD-like acid phosphatase, associated with soybean tolerance to low phosphorus stress. Phosphorus (P) deficiency in soils is a major limiting factor for crop growth worldwide. Plants may adapt to low phosphorus (LP) conditions via changes to root morphology, including the number, length, orientation, and branching of the principal root classes. To elucidate the genetic mechanisms for LP tolerance in soybean, quantitative trait loci (QTL) related to root morphology responses to LP were identified via hydroponic experiments...
May 12, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29753465/short-communication-uncovering-quantitative-trait-loci-associated-with-resistance-to-mycobacterium-avium-ssp-paratuberculosis-infection-in-holstein-cattle-using-a-high-density-single-nucleotide-polymorphism-panel
#19
Sanjay Mallikarjunappa, M Sargolzaei, L F Brito, K G Meade, N A Karrow, S D Pant
Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of Johne's disease in cattle. Johne's disease is a disease of significant economic, animal welfare, and public health concern around the globe. Therefore, understanding the genetic architecture of resistance to MAP infection has great relevance to advance genetic selection methods to breed more resistant animals. The objectives of this study were to perform a genome-wide association study of previously analyzed 50K genotypes now imputed to a high-density single nucleotide polymorphism panel (777K), aiming to validate previously reported associations and potentially identify additional single nucleotide polymorphisms associated with antibody response to MAP infection...
May 9, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29752522/meta-qtl-analysis-of-seed-iron-and-zinc-concentration-and-content-in-common-bean-phaseolus-vulgaris-l
#20
Paulo Izquierdo, Carolina Astudillo, Matthew W Blair, Asif M Iqbal, Bodo Raatz, Karen A Cichy
Twelve meta-QTL for seed Fe and Zn concentration and/or content were identified from 87 QTL originating from seven population grown in sixteen field trials. These meta-QTL include 2 specific to iron, 2 specific to zinc and 8 that co-localize for iron and zinc concentrations and/or content. Common bean (Phaseolus vulgaris L.) is the most important legume for human consumption worldwide and it is an important source of microelements, especially iron and zinc. Bean biofortification breeding programs develop new varieties with high levels of Fe and Zn targeted for countries with human micronutrient deficiencies...
May 11, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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