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https://www.readbyqxmd.com/read/28491067/genome-wide-association-study-reveals-the-genetic-architecture-underlying-salt-tolerance-related-traits-in-rapeseed-brassica-napus-l
#1
Heping Wan, Lunlin Chen, Jianbin Guo, Qun Li, Jing Wen, Bin Yi, Chaozhi Ma, Jinxing Tu, Tingdong Fu, Jinxiong Shen
Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L.) salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS) to identify salt tolerance-related quantitative trait loci (QTL). A natural population comprising 368 B. napus cultivars and inbred lines was genotyped with a Brassica 60K Illumina Infinium SNP array...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28489859/an-r2r3-type-myb-transcription-factor-gmmyb29-regulates-isoflavone-biosynthesis-in-soybean
#2
Shanshan Chu, Jiao Wang, Ying Zhu, Shulin Liu, Xiaoqiong Zhou, Huairen Zhang, Chun-E Wang, Wenming Yang, Zhixi Tian, Hao Cheng, Deyue Yu
Isoflavones comprise a group of secondary metabolites produced almost exclusively by plants in the legume family, including soybean [Glycine max (L.) Merr.]. They play vital roles in plant defense and have many beneficial effects on human health. Isoflavone content is a complex quantitative trait controlled by multiple genes, and the genetic mechanisms underlying isoflavone biosynthesis remain largely unknown. Via a genome-wide association study (GWAS), we identified 28 single nucleotide polymorphisms (SNPs) that are significantly associated with isoflavone concentrations in soybean...
May 10, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28371164/genome-wide-association-study-discovered-candidate-genes-of-verticillium-wilt-resistance-in-upland-cotton-gossypium-hirsutum-l
#3
Tinggang Li, Xuefeng Ma, Nanyang Li, Lei Zhou, Zheng Liu, Huanyong Han, Yuejing Gui, Yuming Bao, Jieyin Chen, Xiaofeng Dai
Verticillium wilt (VW), caused by infection by Verticillium dahliae, is considered one of the most yield-limiting diseases in cotton. To examine the genetic architecture of cotton VW resistance, we performed a genome-wide association study (GWAS) using a panel of 299 accessions and 85,630 single-nucleotide polymorphisms (SNPs) detected using the specific-locus amplified fragment sequencing (SLAF-seq) approach. Trait-SNP association analysis detected a total of 17 significant SNPs at P < 1.17 × 10(-5) (P = 1/85630, -log10 P = 4...
March 29, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28367154/genome-analysis-identified-novel-candidate-genes-for-ascochyta-blight-resistance-in-chickpea-using-whole-genome-re-sequencing-data
#4
Yongle Li, Pradeep Ruperao, Jacqueline Batley, David Edwards, Jenny Davidson, Kristy Hobson, Tim Sutton
Ascochyta blight (AB) is a fungal disease that can significantly reduce chickpea production in Australia and other regions of the world. In this study, 69 chickpea genotypes were sequenced using whole genome re-sequencing (WGRS) methods. They included 48 Australian varieties differing in their resistance ranking to AB, 16 advanced breeding lines from the Australian chickpea breeding program, four landraces, and one accession representing the wild chickpea species Cicer reticulatum. More than 800,000 single nucleotide polymorphisms (SNPs) were identified...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28338805/deciphering-the-genetic-control-of-fruit-texture-in-apple-by-multiple-family-based-analysis-and-genome-wide-association
#5
Mario Di Guardo, Marco C A M Bink, Walter Guerra, Thomas Letschka, Lidia Lozano, Nicola Busatto, Lara Poles, Alice Tadiello, Luca Bianco, Richard G F Visser, Eric van de Weg, Fabrizio Costa
Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions...
March 1, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28321828/genome-wide-association-analysis-tracks-bacterial-leaf-blight-resistance-loci-in-rice-diverse-germplasm
#6
Christine Jade Dilla-Ermita, Erwin Tandayu, Venice Margarette Juanillas, Jeffrey Detras, Dennis Nicuh Lozada, Maria Stefanie Dwiyanti, Casiana Vera Cruz, Edwige Gaby Nkouaya Mbanjo, Edna Ardales, Maria Genaleen Diaz, Merlyn Mendioro, Michael J Thomson, Tobias Kretzschmar
BACKGROUND: A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines...
December 2017: Rice
https://www.readbyqxmd.com/read/28301713/population-structure-and-genetic-basis-of-the-agronomic-traits-of-upland-cotton-in-china-revealed-by-a-genome-wide-association-study-using-high-density-snps
#7
Cong Huang, Xinhui Nie, Chao Shen, Chunyuan You, Wu Li, Wenxia Zhao, Xianlong Zhang, Zhongxu Lin
Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton producing and consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nation-wide population containing 503 G. hirsutum accessions was collected for a genome-wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping...
March 16, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28261256/genome-wide-association-and-transcriptome-analyses-reveal-candidate-genes-underlying-yield-determining-traits-in-brassica-napus
#8
Kun Lu, Liu Peng, Chao Zhang, Junhua Lu, Bo Yang, Zhongchun Xiao, Ying Liang, Xingfu Xu, Cunmin Qu, Kai Zhang, Liezhao Liu, Qinlong Zhu, Minglian Fu, Xiaoyan Yuan, Jiana Li
Yield is one of the most important yet complex crop traits. To improve our understanding of the genetic basis of yield establishment, and to identify candidate genes responsible for yield improvement in Brassica napus, we performed genome-wide association studies (GWAS) for seven yield-determining traits [main inflorescence pod number (MIPN), branch pod number (BPN), pod number per plant (PNP), seed number per pod (SPP), thousand seed weight, main inflorescence yield (MIY), and branch yield], using data from 520 diverse B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28241006/identification-and-validation-of-single-nucleotide-polymorphic-markers-linked-to-ug99-stem-rust-resistance-in-spring-wheat
#9
Long-Xi Yu, Shiaoman Chao, Ravi P Singh, Mark E Sorrells
Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT)...
2017: PloS One
https://www.readbyqxmd.com/read/28223988/the-impact-of-genotyping-by-sequencing-pipelines-on-snp-discovery-and-identification-of-markers-associated-with-verticillium-wilt-resistance-in-autotetraploid-alfalfa-medicago-sativa-l
#10
Long-Xi Yu, Ping Zheng, Suresh Bhamidimarri, Xiang-Ping Liu, Dorie Main
Verticillium wilt (VW) of alfalfa is a soilborne disease causing severe yield loss in alfalfa. To identify molecular markers associated with VW resistance, we used an integrated framework of genome-wide association study (GWAS) with high-throughput genotyping by sequencing (GBS) to identify loci associated with VW resistance in an F1 full-sib alfalfa population. Phenotyping was performed using manual inoculation of the pathogen to cloned plants of each individual and disease severity was scored using a standard scale...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28218981/the-genetic-architecture-of-amino-acids-dissection-by-association-and-linkage-analysis-in-maize
#11
Min Deng, Dongqin Li, Jingyun Luo, Yingjie Xiao, Haijun Liu, Qingchun Pan, Xuehai Zhang, Minliang Jin, Mingchao Zhao, Jianbing Yan
Amino acids are both constituents of proteins, providing the essential nutrition for humans and animals, and signaling molecules regulating the growth and development of plants. Most cultivars of maize are deficient in essential amino acids such as lysine and tryptophan. Here, we measured the levels of 17 different total amino acids, and created 48 derived traits in mature kernels from a maize diversity inbred collection and three recombinant inbred line (RIL) populations. By GWAS, 247 and 281 significant loci were identified in two different environments, 5...
February 20, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28211582/what-can-genome-wide-association-studies-tell-us-about-the-evolutionary-forces-maintaining-genetic-variation-for-quantitative-traits
#12
REVIEW
Emily B Josephs, John R Stinchcombe, Stephen I Wright
Contents 21 I. 21 II. 22 III. 24 IV. 25 V. 29 30 References 30 SUMMARY: Understanding the evolutionary forces that shape genetic variation within species has long been a goal of evolutionary biology. Integrating data for the genetic architecture of traits from genome-wide association mapping studies (GWAS) along with the development of new population genetic methods for identifying selection in sequence data may allow us to evaluate the roles of mutation-selection balance and balancing selection in shaping genetic variation at various scales...
April 2017: New Phytologist
https://www.readbyqxmd.com/read/28188333/use-of-modern-tomato-breeding-germplasm-for-deciphering-the-genetic-control-of-agronomical-traits-by-genome-wide-association-study
#13
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Julien Bonnet, Laurent Grivet, Mathilde Causse
A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato...
February 10, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28152098/genome-wide-association-analysis-for-heat-tolerance-at-flowering-detected-a-large-set-of-genes-involved-in-adaptation-to-thermal-and-other-stresses
#14
Tanguy Lafarge, Crisanta Bueno, Julien Frouin, Laval Jacquin, Brigitte Courtois, Nourollah Ahmadi
Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST) under 38°C during anthesis and for several secondary traits potentially affecting panicle micro-climate and thus the fertilization process. The panel was genotyped with an average density of one marker per 29 kb using genotyping by sequencing. Genome-wide association analyses (GWAS) were conducted using three methods based on single marker regression, haplotype regression and simultaneous fitting of all markers, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28152092/a-genome-wide-association-study-for-agronomic-traits-in-soybean-using-snp-markers-and-snp-based-haplotype-analysis
#15
Rodrigo Iván Contreras-Soto, Freddy Mora, Marco Antônio Rott de Oliveira, Wilson Higashi, Carlos Alberto Scapim, Ivan Schuster
Mapping quantitative trait loci through the use of linkage disequilibrium (LD) in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max). The haplotype-based genome-wide association study (GWAS) has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW), plant height (PH) and seed yield (SY) in a soybean association mapping panel using single nucleotide polymorphism (SNP) markers and haplotype information...
2017: PloS One
https://www.readbyqxmd.com/read/28108698/genome-wide-analysis-of-fatty-acid-desaturation-and-its-response-to-temperature
#16
Guillaume N Menard, Jose Martin Moreno, Fiona M Bryant, Olaya Munoz-Azcarate, Amélie A Kelly, Keywan Hassani-Pak, Smita Kurup, Peter J Eastmond
Plants modify the polyunsaturated fatty acid content of their membrane and storage lipids in order to adapt to changes in temperature. In developing seeds, this response is largely controlled by the activities of the microsomal ω-6 and ω-3 fatty acid desaturases, FAD2 and FAD3. Although temperature regulation of desaturation has been studied at the molecular and biochemical levels, the genetic control of this trait is poorly understood. Here, we have characterized the response of Arabidopsis (Arabidopsis thaliana) seed lipids to variation in ambient temperature and found that heat inhibits both ω-6 and ω-3 desaturation in phosphatidylcholine, leading to a proportional change in triacylglycerol composition...
March 2017: Plant Physiology
https://www.readbyqxmd.com/read/28068350/genome-wide-association-mapping-and-genomic-selection-for-alfalfa-medicago-sativa-forage-quality-traits
#17
Elisa Biazzi, Nelson Nazzicari, Luciano Pecetti, E Charles Brummer, Alberto Palmonari, Aldo Tava, Paolo Annicchiarico
Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest)...
2017: PloS One
https://www.readbyqxmd.com/read/28055148/genome-wide-association-study-for-13-agronomic-traits-reveals-distribution-of-superior-alleles-in-bread-wheat-from-the-yellow-and-huai-valley-of-china
#18
Congwei Sun, Fuyan Zhang, Xuefang Yan, Xiangfen Zhang, Zhongdong Dong, Dangqun Cui, Feng Chen
Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here we revealed new allelic variation distribution for 13 yield-related traits in series of genome-wide association studies (GWAS) using the Wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over three years. After filtering SNP datasets, GWAS using 20,689 high-quality SNPs associated 1,769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions...
January 5, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28039515/genome-wide-association-mapping-for-seedling-and-field-resistance-to-puccinia-striiformis-f-sp-tritici-in-elite-durum-wheat
#19
Weizhen Liu, Marco Maccaferri, Peter Bulli, Sheri Rynearson, Roberto Tuberosa, Xianming Chen, Michael Pumphrey
Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide. Improving resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major objective for wheat breeding. To identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using 232 elite durum wheat (Triticum turgidum ssp. durum) lines from worldwide breeding programs...
April 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27987166/mining-plant-genomic-and-genetic-data-using-the-gnpis-information-system
#20
A-F Adam-Blondon, M Alaux, S Durand, T Letellier, G Merceron, N Mohellibi, C Pommier, D Steinbach, F Alfama, J Amselem, D Charruaud, N Choisne, R Flores, C Guerche, V Jamilloux, E Kimmel, N Lapalu, M Loaec, C Michotey, H Quesneville
GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system...
2017: Methods in Molecular Biology
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