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Zixiang Wen, Ruijuan Tan, Shichen Zhang, Paul J Collins, Jiazheng Yuan, Wenyan Du, Cuihua Gu, Shujun Ou, Qijian Song, Yong-Qiang Charles An, John F Boyse, Martin I Chilvers, Dechun Wang
White mold of soybean, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a necrotrophic fungus capable of infecting a wide range of plants. To dissect the genetic architecture of resistance to white mold, a high-density customized single nucleotide polymorphism (SNP) array (52,041 SNPs) was used to genotype two soybean diversity panels. Combined with resistance variation data observed in the field and greenhouse environments, genome-wide association studies (GWAS) were conducted to identify quantitative trait loci (QTL) controlling resistance against white mold...
March 12, 2018: Plant Biotechnology Journal
Yongle Li, Pradeep Ruperao, Jacqueline Batley, David Edwards, Tanveer Khan, Timothy D Colmer, Jiayin Pang, Kadambot H M Siddique, Tim Sutton
Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs). We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0...
2018: Frontiers in Plant Science
Khaled M Hazzouri, Basel Khraiwesh, Khaled M A Amiri, Duke Pauli, Tom Blake, Mohammad Shahid, Sangeeta K Mullath, David Nelson, Alain L Mansour, Kourosh Salehi-Ashtiani, Michael Purugganan, Khaled Masmoudi
Sodium (Na+ ) accumulation in the cytosol will result in ion homeostasis imbalance and toxicity of transpiring leaves. Studies of salinity tolerance in the diploid wheat ancestor Triticum monococcum showed that HKT1;5 -like gene was a major gene in the QTL for salt tolerance, named Nax2 . In the present study, we were interested in investigating the molecular mechanisms underpinning the role of the HKT1;5 gene in salt tolerance in barley ( Hordeum vulgare ). A USDA mini-core collection of 2,671 barley lines, part of a field trial was screened for salinity tolerance, and a Genome Wide Association Study (GWAS) was performed...
2018: Frontiers in Plant Science
Francois Laurens, Maria José Aranzana, Pere Arus, Daniele Bassi, Marco Bink, Joan Bonany, Andrea Caprera, Luca Corelli-Grappadelli, Evelyne Costes, Charles-Eric Durel, Jehan-Baptiste Mauroux, Hélène Muranty, Nelson Nazzicari, Thierry Pascal, Andrea Patocchi, Andreas Peil, Bénédicte Quilot-Turion, Laura Rossini, Alessandra Stella, Michela Troggio, Riccardo Velasco, Eric van de Weg
Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders...
2018: Horticulture Research
Junji Su, Libei Li, Chi Zhang, Caixiang Wang, Lijiao Gu, Hantao Wang, Hengling Wei, Qibao Liu, Long Huang, Shuxun Yu
Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton. A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting...
March 1, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Peter S Kristensen, Ahmed Jahoor, Jeppe R Andersen, Fabio Cericola, Jihad Orabi, Luc L Janss, Just Jensen
The aim of the this study was to identify SNP markers associated with five important wheat quality traits (grain protein content, Zeleny sedimentation, test weight, thousand-kernel weight, and falling number), and to investigate the predictive abilities of GBLUP and Bayesian Power Lasso models for genomic prediction of these traits. In total, 635 winter wheat lines from two breeding cycles in the Danish plant breeding company Nordic Seed A/S were phenotyped for the quality traits and genotyped for 10,802 SNPs...
2018: Frontiers in Plant Science
Asis Shrestha, Ambrose Kwaku Dziwornu, Yoshiaki Ueda, Lin-Bo Wu, Boby Mathew, Michael Frei
Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn2+ leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn2+, 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2...
2018: PloS One
Ana M Bossa-Castro, Cheick Tekete, Chitra Raghavan, Emily E Delorean, Alexis Dereeper, Karim Dagno, Ousmane Koita, Gloria Mosquera, Hei Leung, Valérie Verdier, Jan E Leach
Quantitative trait loci (QTL) that confer broad-spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programs. Multi-parent Advanced Generation Inter-Cross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv...
February 6, 2018: Plant Biotechnology Journal
Weiwei Wen, Min Jin, Kun Li, Haijun Liu, Yingjie Xiao, Mingchao Zhao, Saleh Alseekh, Wenqiang Li, Francisco de Abreu E Lima, Yariv Brotman, Lothar Willmitzer, Alisdair R Fernie, Jianbing Yan
Primary metabolism plays pivotal roles in normal plant growth, development, and reproduction. As maize is a major crop worldwide, the primary metabolites produced by maize plants are of immense importance from calorific and nutritional perspectives. Here a genome-wide association study (GWAS) of 61 primary metabolites using a maize association panel containing 513 inbred lines identified 153 significant loci associated with the level of these metabolites in four independent tissues. The genome-wide expression level of 760 genes were also linked with metabolite levels within the same tissue...
January 30, 2018: Plant Journal: for Cell and Molecular Biology
Girum Azmach, Abebe Menkir, Charles Spillane, Melaku Gedil
The discovery and use of genetic markers associated with carotenoid levels can help to more effectively exploit the genetic potential of maize for provitamin A accumulation. Provitamin A carotenoids are classes of carotenoids that are precursors of vitamin A, an essential micronutrient in humans. Vitamin A deficiency is a global public health problem affecting millions of people, especially in developing countries. Maize is one of the most important staple crops targeted for provitamin A biofortification to help alleviate vitamin A deficiency in developing countries...
January 29, 2018: G3: Genes—Genomes—Genetics
Muhammad ArslanAnwer, Muhammad Shahzad Anjam, Syed Jehangir Shah, M Shamim Hasan, Ali A Naz, Florian M W Grundler, Shahid Siddique
Plant-parasitic cyst nematodes are obligate sedentary parasites that infect the roots of a broad range of host plants. Cyst nematodes are sexually dimorphic, but differentiation into male or female is strongly influenced by interactions with the host environment. Female populations typically predominate under favorable conditions, whereas male populations predominate under adverse conditions. Here, we performed a genome-wide association study (GWAS) in an Arabidopsis diversity panel to identify host loci underlying variation in susceptibility to cyst nematode infection...
January 25, 2018: Journal of Experimental Botany
Zhigang Han, Jingjie Zhang, Shengguan Cai, Xiaohui Chen, Xiaoyan Quan, Guoping Zhang
BACKGROUND: The interest has been increasing on the phenolic compounds in plants because of their nutritive function as food and the roles regulating plant growth. However, their underlying genetic mechanism in barley is still not clear. RESULTS: A genome-wide association study (GWAS) was conducted for total phenolic content (TPC), total flavonoid content (FLC) and antioxidant activity (AOA) in 67 cultivated and 156 Tibetan wild barley genotypes. Most markers associated with phenolic content were different in cultivated and wild barleys...
January 25, 2018: BMC Genomics
Siraj Ismail Kayondo, Dunia Pino Del Carpio, Roberto Lozano, Alfred Ozimati, Marnin Wolfe, Yona Baguma, Vernon Gracen, Samuel Offei, Morag Ferguson, Robert Kawuki, Jean-Luc Jannink
Cassava (Manihot esculenta Crantz) is an important security crop that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genetic improvement of cassava is undergoing rapid change due to the implementation of quantitative trait loci mapping, Genome-wide association mapping (GWAS), and genomic selection (GS). In this study, two breeding panels were genotyped for SNP markers using genotyping by sequencing and phenotyped for foliar and CBSD root symptoms at five locations in Uganda...
January 24, 2018: Scientific Reports
Lianne Merchuk-Ovnat, Roi Silberman, Efrat Laiba, Andreas Maurer, Klaus Pillen, Adi Faigenboim, Eyal Fridman
Increasing crop productivity under climate change requires the identification, selection and utilization of novel alleles for breeding. We analyzed the genotype and field phenotype of the barley HEB-25 multi-parent mapping population under well-watered and water-limited (WW and WL) environments for two years. A genome-wide association study (GWAS) for genotype by-environment interactions was performed for ten traits including flowering time (HEA) and plant grain yield (PGY). Comparison of the GWAS for traits per-se to that for QTL-by-environment interactions (QxE), indicates the prevalence of QxE mostly for reproductive traits...
January 20, 2018: Journal of Experimental Botany
Darlene L Sanchez, Sisi Liu, Rania Ibrahim, Michael Blanco, Thomas Lübberstedt
Root system architecture (RSA) is becoming recognized as important for water and nutrient acquisition in plants. This study focuses on finding single nucleotide polymorphisms (SNPs) associated with seedling RSA traits from 300 doubled haploid (DH) lines derived from crosses between Germplasm Enhancement of Maize (GEM) accessions and inbred lines PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers, while root and shoot phenotype data were collected from 14-day old seedlings. Genome-wide association studies (GWAS) were conducted using three models to offset false positives/negatives...
March 2018: Plant Science: An International Journal of Experimental Plant Biology
Paul Herzig, Andreas Maurer, Vera Draba, Rajiv Sharma, Fulvia Draicchio, Hazel Bull, Linda Milne, William T B Thomas, Andrew J Flavell, Klaus Pillen
Barley is cultivated more widely than the other major world crops because it adapts well to environmental constraints, such as drought, heat and day length. To better understand the genetic control of local adaptation in barley, we studied development in the nested association mapping population HEB-25, derived from crossing 25 wild barleys with the cultivar Barke. HEB-25 was cultivated in replicated field trials in Dundee (Scotland) and Halle (Germany) differing in regard to day length, precipitation and temperature...
January 18, 2018: Journal of Experimental Botany
Hong Wang, Shutu Xu, Yaming Fan, Nannan Liu, Wei Zhan, Haijun Liu, Yingjie Xiao, Kun Li, Qingchun Pan, Wenqiang Li, Min Deng, Jie Liu, Min Jin, Xiaohong Yang, Jiansheng Li, Qing Li, Jianbing Yan
Although tocopherols play an important role in plants and animals, the genetic architecture of tocopherol content in maize kernels has remained largely unknown. In this study, linkage and association analyses were conducted to examine the genetic architecture of tocopherol content in maize kernels. Forty-one unique quantitative trait loci (QTLs) were identified by linkage mapping in six populations of recombinant inbred lines (RILs). In addition, 32 significant loci were detected via genome-wide association study (GWAS), 18 of which co-localized with the QTLs identified by linkage mapping...
January 21, 2018: Plant Biotechnology Journal
Ahmad M Alqudah, Helmy M Youssef, Andreas Graner, Thorsten Schnurbusch
GWAS analysis for leaf blade area (LA) revealed intriguing genomic regions associated with putatively novel QTL and known plant stature-related phytohormone and sugar-related genes. Despite long-standing studies in the morpho-physiological characters of leaf blade area (LA) in cereal crops, advanced genetic studies to explore its natural variation are lacking. The importance of modifying LA in improving cereal grain yield and the genes controlling leaf traits have been well studied in rice but not in temperate cereals...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Moysés Nascimento, Ana Carolina Campana Nascimento, Fabyano Fonseca E Silva, Leiri Daiane Barili, Naine Martins do Vale, José Eustáquio Carneiro, Cosme Damião Cruz, Pedro Crescêncio Souza Carneiro, Nick Vergara Lopes Serão
Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower-DFF; Days for flowering-DTF; Days to end of flowering-DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons...
2018: PloS One
Envel Kerdaffrec, Magnus Nordborg
Seed dormancy is a complex adaptive trait that controls the timing of seed germination, one of the major fitness components in many plant species. Despite being highly heritable, seed dormancy is extremely plastic and influenced by a wide range of environmental cues. Here, using a set of 92 Arabidopsis thaliana lines from Sweden, we investigate the effect of seed maturation temperature on dormancy variation at the population level. The response to temperature differs dramatically between lines, demonstrating that genotype and the maternal environment interact in controlling the trait...
2017: PloS One
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