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https://www.readbyqxmd.com/read/28797221/use-of-genotyping-by-sequencing-to-determine-the-genetic-structure-in-the-medicinal-plant-chamomile-and-to-identify-flowering-time-and-alpha-bisabolol-associated-snp-loci-by-genome-wide-association-mapping
#1
Lars-Gernot Otto, Prodyut Mondal, Jonathan Brassac, Susanne Preiss, Jörg Degenhardt, Sang He, Jochen Christoph Reif, Timothy Francis Sharbel
BACKGROUND: Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active. In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28770301/genome-wide-association-mapping-reveals-a-rich-genetic-architecture-of-stripe-rust-resistance-loci-in-emmer-wheat-triticum-turgidum-ssp-dicoccum
#2
Weizhen Liu, Marco Maccaferri, Xianming Chen, Gaetano Laghetti, Domenico Pignone, Michael Pumphrey, Roberto Tuberosa
SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated...
August 2, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28769955/genome-wide-association-study-reveals-candidate-genes-for-control-of-plant-height-branch-initiation-height-and-branch-number-in-rapeseed-brassica-napus-l
#3
Ming Zheng, Cheng Peng, Hongfang Liu, Min Tang, Hongli Yang, Xiaokang Li, Jinglin Liu, Xingchao Sun, Xinfa Wang, Junfeng Xu, Wei Hua, Hanzhong Wang
Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number (BN) and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH, and BN) in a panel of 333 rapeseed accessions across 4 years. A genome-wide association study (GWAS) was performed via Q + K model and the panel was genotyped using the 60 k Brassica Infinium SNP array. We identified seven loci for PH, four for BIH, and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15, and 17 candidate genes for these traits, respectively...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747922/identification-of-major-quantitative-trait-loci-for-seed-oil-content-in-soybeans-by-combining-linkage-and-genome-wide-association-mapping
#4
Yongce Cao, Shuguang Li, Zili Wang, Fangguo Chang, Jiejie Kong, Junyi Gai, Tuanjie Zhao
Soybean oil is the most widely produced vegetable oil in the world and its content in soybean seed is an important quality trait in breeding programs. More than 100 quantitative trait loci (QTLs) for soybean oil content have been identified. However, most of them are genotype specific and/or environment sensitive. Here, we used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28727806/genocore-a-simple-and-fast-algorithm-for-core-subset-selection-from-large-genotype-datasets
#5
Seongmun Jeong, Jae-Yoon Kim, Soon-Chun Jeong, Sung-Taeg Kang, Jung-Kyung Moon, Namshin Kim
Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset...
2017: PloS One
https://www.readbyqxmd.com/read/28724078/genome-wide-association-study-of-developing-leaves-heat-tolerance-during-vegetative-growth-stages-in-a-sorghum-association-panel
#6
Junping Chen, Ratan Chopra, Chad Hayes, Geoffrey Morris, Sandeep Marla, John Burke, Zhanguo Xin, Gloria Burow
Heat stress reduces grain yield and quality worldwide. Enhancing heat tolerance of crops at all developmental stages is one of the essential strategies required for sustaining agricultural production especially as frequency of temperature extremes escalates in response to climate change. Although heat tolerance mechanisms have been studied extensively in model plant species, little is known about the genetic control underlying heat stress responses of crop plants at the vegetative stage under field conditions...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28712931/genome-wide-association-study-reveals-that-the-aquaporin-nip1-1-contributes-to-variation-in-hydrogen-peroxide-sensitivity-in-arabidopsis-thaliana
#7
Ayan Sadhukhan, Yuriko Kobayashi, Yuki Nakano, Satoshi Iuchi, Masatomo Kobayashi, Lingaraj Sahoo, Hiroyuki Koyama
Hydrogen peroxide (H2O2) is a reactive oxygen species that affects cell signaling in various plant defense responses and induces programmed cell death. To identify the new components associated with H2O2 signaling and tolerance, we conducted a genome-wide association study (GWAS) on the root growth of 133 Arabidopsis thaliana accessions grown in the presence of toxic H2O2 levels. The most significant SNPs were associated with a cluster of chromosome 4 genes encoding an aquaporin NODULIN 26-LIKE INTRINSIC PROTEIN 1; 1 (NIP1;1), an NB-ARC domain-containing disease resistance protein (AT4G19050), and a putative membrane lipoprotein (AT4G19070)...
August 7, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28710561/genetic-architecture-of-wild-soybean-glycine-soja-response-to-soybean-cyst-nematode-heterodera-glycines
#8
Hengyou Zhang, Qijian Song, Joshua D Griffin, Bao-Hua Song
The soybean cyst nematode (SCN) is one of the most destructive pathogens of soybean plants worldwide. Host-plant resistance is an environmentally friendly method to mitigate SCN damage. To date, the resistant soybean cultivars harbor limited genetic variation, and some are losing resistance. Thus, a better understanding of the genetic mechanisms of the SCN resistance, as well as developing diverse resistant soybean cultivars, is urgently needed. In this study, a genome-wide association study (GWAS) was conducted using 1032 wild soybean (Glycine soja) accessions with over 42,000 single-nucleotide polymorphisms (SNPs) to understand the genetic architecture of G...
July 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28696287/genomic-architecture-of-biomass-heterosis-in-arabidopsis
#9
Mei Yang, Xuncheng Wang, Diqiu Ren, Hao Huang, Miqi Xu, Guangming He, Xing Wang Deng
Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 Arabidopsis hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids...
July 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28684880/genomic-and-phenotypic-analysis-of-vavilov-s-historic-landraces-reveals-the-impact-of-environment-and-genomic-islands-of-agronomic-traits
#10
Elena Plekhanova, Margarita A Vishnyakova, Sergey Bulyntsev, Peter L Chang, Noelia Carrasquilla-Garcia, Kassaye Negash, Eric von Wettberg, Nina Noujdina, Douglas R Cook, Maria G Samsonova, Sergey V Nuzhdin
The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28667309/an-integrated-hyperspectral-imaging-and-genome-wide-association-analysis-platform-provides-spectral-and-genetic-insights-into-the-natural-variation-in-rice
#11
Hui Feng, Zilong Guo, Wanneng Yang, Chenglong Huang, Guoxing Chen, Wei Fang, Xiong Xiong, Hongyu Zhang, Gongwei Wang, Lizhong Xiong, Qian Liu
With progress of genetic sequencing technology, plant genomics has experienced rapid development and subsequently triggered the progress of plant phenomics. In this study, a high-throughput hyperspectral imaging system (HHIS) was developed to obtain 1,540 hyperspectral indices at whole-plant level during tillering, heading, and ripening stages. These indices were used to quantify traditional agronomic traits and to explore genetic variation. We performed genome-wide association study (GWAS) of these indices and traditional agronomic traits in a global rice collection of 529 accessions...
June 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642772/assessment-of-five-chilling-tolerance-traits-and-gwas-mapping-in-rice-using-the-usda-mini-core-collection
#12
Michael R Schläppi, Aaron K Jackson, Georgia C Eizenga, Aiju Wang, Chengcai Chu, Yao Shi, Naoki Shimoyama, Debbie L Boykin
Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28620159/main-and-epistatic-loci-studies-in-soybean-for-sclerotinia-sclerotiorum-resistance-reveal-multiple-modes-of-resistance-in-multi-environments
#13
Tara C Moellers, Arti Singh, Jiaoping Zhang, Jae Brungardt, Mehdi Kabbage, Daren S Mueller, Craig R Grau, Ashish Ranjan, Damon L Smith, R V Chowda-Reddy, Asheesh K Singh
Genome-wide association (GWAS) and epistatic (GWES) studies along with expression studies in soybean [Glycine max (L.) Merr.] were leveraged to dissect the genetics of Sclerotinia stem rot (SSR) [caused by Sclerotinia sclerotiorum (Lib.) de Bary], a significant fungal disease causing yield and quality losses. A large association panel of 466 diverse plant introduction accessions were phenotyped in multiple field and controlled environments to: (1) discover sources of resistance, (2) identify SNPs associated with resistance, and (3) determine putative candidate genes to elucidate the mode of resistance...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28600722/genetic-dissection-of-plant-growth-habit-in-chickpea
#14
Hari D Upadhyaya, Deepak Bajaj, Rishi Srivastava, Anurag Daware, Udita Basu, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs...
June 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28596776/genome-wide-association-mapping-of-loci-associated-with-plant-growth-and-forage-production-under-salt-stress-in-alfalfa-medicago-sativa-l
#15
Xiang-Ping Liu, Long-Xi Yu
Salinity tolerance is highly desirable to sustain alfalfa production in marginal lands that have been rendered saline. In this study, we used a diverse panel of 198 alfalfa accessions for mapping loci associated with plant growth and forage production under salt stress using genome-wide association studies (GWAS). The plants were genotyped using genotyping-by-sequencing (GBS). A greenhouse procedure was used for phenotyping four agronomic and physiological traits affected by salt stress, including dry weight (DW), plant height (PH), leaf chlorophyll content (LCC), and stomatal conductance (SC)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28591221/loci-associated-with-resistance-to-stripe-rust-puccinia-striiformis-f-sp-tritici-in-a-core-collection-of-spring-wheat-triticum-aestivum
#16
Kebede T Muleta, Peter Bulli, Sheri Rynearson, Xianming Chen, Michael Pumphrey
Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) remains one of the most significant diseases of wheat worldwide. We investigated stripe rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28585324/identification-of-major-loci-and-genomic-regions-controlling-acid-and-volatile-content-in-tomato-fruit-implications-for-flavor-improvement
#17
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Vincent Segura, Aniko Kende, Jules Beekwilder, Katarina Cankar, Jean-Luc Gallois, Justine Gricourt, Julien Bonnet, Charles Baxter, Laurent Grivet, Mathilde Causse
Plant metabolites are important to world food security due to their roles in crop yield and nutritional quality. Here we report the metabolic profile of 300 tomato accessions (Solanum lycopersicum and related wild species) by quantifying 60 primary and secondary metabolites, including volatile organic compounds, over a period of 2 yr. Metabolite content and genetic inheritance of metabolites varied broadly, both within and between different genetic groups. Using genotype information gained from 10 000 single nucleotide polymorphism markers, we performed a metabolite genome-wide association mapping (GWAS) study...
June 6, 2017: New Phytologist
https://www.readbyqxmd.com/read/28559904/genetic-architecture-of-anther-extrusion-in-spring-and-winter-wheat
#18
Quddoos H Muqaddasi, Jonathan Brassac, Andreas Börner, Klaus Pillen, Marion S Röder
Hybrid wheat breeding is gaining prominence worldwide because it ensures higher and more static yield than conventionally bred varieties. The cleistogamous floral architecture of wheat (Triticum aestivum L.) impedes anthers inside the floret, making it largely an inbreeder. For hybrid seed production, high anther extrusion is needed to promote cross pollination and to ensure a high level of pollen availability for the seed plant. This study, therefore, aimed at the genetic dissection of anther extrusion (AE) in panels of spring (SP), and winter wheat (WP) accessions by genome wide association studies (GWAS)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28553306/novel-sources-of-stripe-rust-resistance-identified-by-genome-wide-association-mapping-in-ethiopian-durum-wheat-triticum-turgidum-ssp-durum
#19
Weizhen Liu, Marco Maccaferri, Sheri Rynearson, Tesfaye Letta, Habtemariam Zegeye, Roberto Tuberosa, Xianming Chen, Michael Pumphrey
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is a global concern for wheat production, and has been increasingly destructive in Ethiopia, as well as in the United States and in many other countries. As Ethiopia has a long history of stripe rust epidemics, its native wheat germplasm harbors potentially valuable resistance loci. Moreover, the Ethiopian germplasm has been historically underutilized in breeding of modern wheat worldwide and thus the resistance alleles from the Ethiopian germplasm represent potentially novel sources...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28491067/genome-wide-association-study-reveals-the-genetic-architecture-underlying-salt-tolerance-related-traits-in-rapeseed-brassica-napus-l
#20
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
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