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Quantitative trait loci

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https://www.readbyqxmd.com/read/28813538/genome-wide-association-analysis-reveals-genetic-loci-and-candidate-genes-for-feeding-behavior-and-eating-efficiency-in-duroc-boars
#1
Rongrong Ding, Jianping Quan, Ming Yang, Xingwang Wang, Enqin Zheng, Huaqiang Yang, Disheng Fu, Yang Yang, Linxue Yang, Zicong Li, Dewu Liu, Gengyuan Cai, Zhenfang Wu, Jie Yang
Efficient use of feed resources is a challenge in the pork industry because the largest variability in expenditure is attributed to the cost of fodder. Efficiency of feeding is directly related to feeding behavior. In order to identify genomic regions controlling feeding behavior and eating efficiency traits, 338 Duroc boars were used in this study. The Illumina Porcine SNP60K BeadChip was used for genotyping. Data pertaining to individual daily feed intake (DFI), total daily time spent in feeder (TPD), number of daily visits to feeder (NVD), average duration of each visit (TPV), mean feed intake per visit (FPV), mean feed intake rate (FR), and feed conversion ratio (FCR) were collected for these pigs...
2017: PloS One
https://www.readbyqxmd.com/read/28812690/young-inversion-with-multiple-linked-qtls-under-selection-in-a-hybrid-zone
#2
Cheng-Ruei Lee, Baosheng Wang, Julius P Mojica, Terezie Mandáková, Kasavajhala V S K Prasad, Jose Luis Goicoechea, Nadeesha Perera, Uffe Hellsten, Hope N Hundley, Jenifer Johnson, Jane Grimwood, Kerrie Barry, Stephen Fairclough, Jerry W Jenkins, Yeisoo Yu, Dave Kudrna, Jianwei Zhang, Jayson Talag, Wolfgang Golser, Kathryn Ghattas, M Eric Schranz, Rod Wing, Martin A Lysak, Jeremy Schmutz, Daniel S Rokhsar, Thomas Mitchell-Olds
Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta...
April 3, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811544/mutations-in-the-promoter-intron-and-cds-of-two-fad2-generate-multiple-alleles-modulating-linoleic-acid-level-in-yellow-mustard
#3
Fangqin Zeng, Vicky Roslinsky, Bifang Cheng
Linoleic acid (C18:2) is an important polyunsaturated fatty acid in the seed oil of many crops. Here, we report that mutations in the promoter, intron and CDS of the FAD2 genes SalFAD2.LIA1 and SalFAD2.LIA2 generate three alleles LIA (1a) , LIA (1b) and lia (1) and two alleles LIA (2) and lia (2), respectively, controlling the C18:2 variation (4.4-32.7%) in yellow mustard. The allelic effect on increasing C18:2 content is LIA (1a)  > LIA (1b)  > lia (1) , LIA (2) > lia (2), and LIA (1a)  > LIA (2)...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811498/genome-re-sequencing-reveals-the-history-of-apple-and-supports-a-two-stage-model-for-fruit-enlargement
#4
Naibin Duan, Yang Bai, Honghe Sun, Nan Wang, Yumin Ma, Mingjun Li, Xin Wang, Chen Jiao, Noah Legall, Linyong Mao, Sibao Wan, Kun Wang, Tianming He, Shouqian Feng, Zongying Zhang, Zhiquan Mao, Xiang Shen, Xiaoliu Chen, Yuanmao Jiang, Shujing Wu, Chengmiao Yin, Shunfeng Ge, Long Yang, Shenghui Jiang, Haifeng Xu, Jingxuan Liu, Deyun Wang, Changzhi Qu, Yicheng Wang, Weifang Zuo, Li Xiang, Chang Liu, Daoyuan Zhang, Yuan Gao, Yimin Xu, Kenong Xu, Thomas Chao, Gennaro Fazio, Huairui Shu, Gan-Yuan Zhong, Lailiang Cheng, Zhangjun Fei, Xuesen Chen
Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an "ancient" isolated ecotype not directly contributing to apple domestication...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811335/the-conserved-and-unique-genetic-architecture-of-kernel-size-and-weight-in-maize-and-rice
#5
Jie Liu, Juan Huang, Huan Guo, Liu Lan, Hongze Wang, Yuancheng Xu, Xiaohong Yang, Wenqiang Li, Hao Tong, Yingjie Xiao, Qingchun Pan, Feng Qiao, Mohammad Sharif Raihan, Haijun Liu, Xuehai Zhang, Ning Yang, Xiaqing Wang, Min Deng, Minliang Jin, Lijun Zhao, Xin Luo, Yang Zhou, Xiang Li, Wei Zhan, Nannan Liu, Hong Wang, Gengshen Chen, Qing Li, Jianbing Yan
Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28810834/multiple-trait-qtl-mapping-and-genomic-prediction-for-wool-traits-in-sheep
#6
Sunduimijid Bolormaa, Andrew A Swan, Daniel J Brown, Sue Hatcher, Nasir Moghaddar, Julius H van der Werf, Michael E Goddard, Hans D Daetwyler
BACKGROUND: The application of genomic selection to sheep breeding could lead to substantial increases in profitability of wool production due to the availability of accurate breeding values from single nucleotide polymorphism (SNP) data. Several key traits determine the value of wool and influence a sheep's susceptibility to fleece rot and fly strike. Our aim was to predict genomic estimated breeding values (GEBV) and to compare three methods of combining information across traits to map polymorphisms that affect these traits...
August 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28807804/joint-parameter-estimation-in-the-qtl-mapping-of-ordinal-traits
#7
Xiaona Sheng, Yihong Qiu, Ying Zhou, Wensheng Zhu
With the rapid development of statistical genetics, the deep researches of ordinal traits have been gradually emphasized. The data of these traits bear relatively less information than those of continuous phenotypes, therefore it is more complex to map the quantitative trait loci (QTL) of ordinal traits. In this paper, the multiple-interval mapping method is considered in the genetic mapping of ordinal traits. By combining threshold model and statistical model, we build a cumulative logistic regression model to express the relationship between the ordinal data and the QTL genotypes...
August 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28806927/mapping-of-a-major-qtl-for-salt-tolerance-of-mature-field-grown-maize-plants-based-on-snp-markers
#8
Meijie Luo, Yanxin Zhao, Ruyang Zhang, Jinfeng Xing, Minxiao Duan, Jingna Li, Naishun Wang, Wenguang Wang, Shasha Zhang, Zhihui Chen, Huasheng Zhang, Zi Shi, Wei Song, Jiuran Zhao
BACKGROUND: Salt stress significantly restricts plant growth and production. Maize is an important food and economic crop but is also a salt sensitive crop. Identification of the genetic architecture controlling salt tolerance facilitates breeders to select salt tolerant lines. However, the critical quantitative trait loci (QTLs) responsible for the salt tolerance of field-grown maize plants are still unknown. RESULTS: To map the main genetic factors contributing to salt tolerance in mature maize, a double haploid population (240 individuals) and 1317 single nucleotide polymorphism (SNP) markers were employed to produce a genetic linkage map covering 1462...
August 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28805909/genomewide-association-study-for-production-and-meat-quality-traits-in-canchim-beef-cattle
#9
G G Santiago, F Siqueira, F F Cardoso, L C A Regitano, R Ventura, B P Sollero, M D Souza, F B Mokry, A B R Ferreira, R A A Torres
The commercial value of the bovine carcass is determined by a set of traits, such as weight, yield, back fat thickness, and marbling; therefore, the genetic improvement of growth, meat, and carcass quality traits is an important tool to add value to the supply chain. Genomewide association studies (GWAS) enable the identification of loci that control phenotypic expression of quantitative traits (QTL). Therefore, the objective of this work was to perform a GWAS to identify genomic regions and genes associated with growth, carcass traits, and meat quality in Canchim beef cattle...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28805827/transcriptional-risk-scores-link-gwas-to-eqtls-and-predict-complications-in-crohn-s-disease
#10
Urko M Marigorta, Lee A Denson, Jeffrey S Hyams, Kajari Mondal, Jarod Prince, Thomas D Walters, Anne Griffiths, Joshua D Noe, Wallace V Crandall, Joel R Rosh, David R Mack, Richard Kellermayer, Melvin B Heyman, Susan S Baker, Michael C Stephens, Robert N Baldassano, James F Markowitz, Mi-Ok Kim, Marla C Dubinsky, Judy Cho, Bruce J Aronow, Subra Kugathasan, Greg Gibson
Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohn's disease...
August 14, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28803857/mapping-of-quantitative-trait-loci-for-temporal-growth-and-age-at-maturity-in-coho-salmon-evidence-for-genotype-by-sex-interactions
#11
Miyako Kodama, Jeffrey J Hard, Kerry A Naish
Phenotypic differences between males and females are ubiquitous throughout the animal kingdom. Therefore, investigating the extent to which sex-dependent genetic effects contribute to phenotypic variation is important in understanding the evolutionary response of each sex to natural and artificial selection. Sex-specific differences in growth patterns and age at sexual maturity have been observed in a number of anadromous salmonid fishes. In these species, faster growing individuals in a given cohort often mature earlier than conspecifics, and earlier maturing individuals are often males...
August 10, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28801813/detection-of-qtl-for-greasy-fleece-weight-in-sheep-using-a-50%C3%A2-k-single-nucleotide-polymorphism-chip
#12
Fatemeh Ebrahimi, Mohsen Gholizadeh, Ghodrat Rahimi-Mianji, Ayoub Farhadi
Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight...
August 11, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28801731/molecular-mapping-and-genomics-of-soybean-seed-protein-a-review-and-perspective-for-the-future
#13
REVIEW
Gunvant Patil, Rouf Mian, Tri Vuong, Vince Pantalone, Qijian Song, Pengyin Chen, Grover J Shannon, Tommy C Carter, Henry T Nguyen
Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr...
August 11, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28799029/detecting-the-qtl-allele-system-conferring-flowering-date-in-a-nested-association-mapping-population-of-soybean-using-a-novel-procedure
#14
Shuguang Li, Yongce Cao, Jianbo He, Tuanjie Zhao, Junyi Gai
The RTM-GWAS was chosen among five procedures to identify DTF QTL-allele constitution in a soybean NAM population; 139 QTLs with 496 alleles accounting for 81.7% of phenotypic variance were detected. Flowering date (days to flowering, DTF) is an ecological trait in soybean, closely related to its ability to adapt to areas. A nested association mapping (NAM) population consisting of four RIL populations (LM, ZM, MT and MW with M8206 as their common parent) was established and tested for their DTF under five environments...
August 10, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28798752/qtl-analysis-and-nested-association-mapping-for-adult-plant-resistance-to-powdery-mildew-in-two-bread-wheat-populations
#15
Yan Ren, Weixiu Hou, Caixia Lan, Bhoja R Basnet, Ravi P Singh, Wei Zhu, Xiyong Cheng, Dangqun Cui, Feng Chen
CIMMYT wheat (Triticum aestivum L.) lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR) to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL) populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014-2015 and 2015-2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers) and DArT (diversity arrays technology) markers...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28798311/genomic-regions-and-genes-related-to-inter-population-differences-in-body-size-in-the-ground-beetle-carabus-japonicus
#16
Ryohei Komurai, Tomochika Fujisawa, Yutaka Okuzaki, Teiji Sota
Body size is a key trait in diversification among animal species, and revealing the gene regions responsible for body size diversification among populations or related species is important in evolutionary biology. We explored the genomic regions associated with body size differences in Carabus japonicus ground beetle populations by quantitative trait locus (QTL) mapping of F2 hybrids from differently sized parents from two populations using restriction site-associated DNA sequencing and de novo assembly of the beetle whole genome...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797222/genetic-architecture-and-temporal-patterns-of-biomass-accumulation-in-spring-barley-revealed-by-image-analysis
#17
Kerstin Neumann, Yusheng Zhao, Jianting Chu, Jens Keilwagen, Jochen C Reif, Benjamin Kilian, Andreas Graner
BACKGROUND: Genetic mapping of phenotypic traits generally focuses on a single time point, but biomass accumulates continuously during plant development. Resolution of the temporal dynamics that affect biomass recently became feasible using non-destructive imaging. RESULTS: With the aim to identify key genetic factors for vegetative biomass formation from the seedling stage to flowering, we explored growth over time in a diverse collection of two-rowed spring barley accessions...
August 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28796413/complex-genetic-control-of-lung-tumorigenesis-in-resistant-mice-strains
#18
Alice Dassano, Giulia Pintarelli, Chiara E Cotroneo, Angela Pettinicchio, Elena Forcati, Loris De Cecco, Andrea Borrego, Francesca Colombo, Tommaso A Dragani, Giacomo Manenti
The SM/J mouse strain is resistant to chemically induced lung tumorigenesis despite having a haplotype, in the pulmonary adenoma susceptibility locus (Pas1) locus, that confers tumor susceptibility in other strains. To clarify this inconsistent genotype-phenotype correlation, we crossed SM/J mice with another resistant strain and did genome-wide linkage analysis in the (C57BL/6J x SM/J)F2 progeny exposed to urethane to induce lung tumors. Overall, >80% of F2 mice of both sexes developed from 1 to 20 lung tumors...
August 10, 2017: Cancer Science
https://www.readbyqxmd.com/read/28795235/impact-of-seed-protein-alleles-from-three-soybean-sources-on-seed-composition-and-agronomic-traits
#19
Lillian F Brzostowski, Timothy I Pruski, James E Specht, Brian W Diers
Evaluation of seed protein alleles in soybean populations showed that an increase in protein concentration is generally associated with a decrease in oil concentration and yield. Soybean [Glycine max (L.) Merrill] meal is one of the most important plant-based protein sources in the world. Developing cultivars high in seed protein concentration and seed yield is a difficult task because the traits have an inverse relationship. Over two decades ago, a protein quantitative trait loci (QTL) was mapped on chromosome (chr) 20, and this QTL has been mapped to the same position in several studies and given the confirmed QTL designation cqSeed protein-003...
August 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28794258/genetic-architecture-and-molecular-networks-underlying-leaf-thickness-in-desert-adapted-tomato
#20
Viktoriya Coneva, Margaret Frank, Maria A de Luis Balaguer, Mao Li, Rosangela Sozzani, Daniel H Chitwood
Thicker leaves allow plants to grow in water-limited conditions. However, our understanding of the genetic underpinnings of this highly functional leaf shape trait is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato species Solanum pennellii, and identified quantitative trait loci (QTL). We report evidence of a complex genetic architecture of this trait and roles for both genetic and environmental factors...
August 9, 2017: Plant Physiology
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