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Hongwu Wang, Kun Li, Xiaojiao Hu, Zhifang Liu, Yujin Wu, Changling Huang
BACKGROUND: Plant digestibility of silage maize (Zea mays L.) has a large influence on nutrition intake for animal feeding. Improving forage quality will enhance the utilization efficiency and feeding value of forage maize. Dissecting the genetic basis of forage quality will improve our understanding of the complex nature of cell wall biosynthesis and degradation, which is also helpful for breeding good quality silage maize. RESULTS: Acid detergent fiber (ADF), neutral detergent fiber (NDF) and in vitro dry matter digestibility (IVDMD) of stalk were evaluated in a diverse maize population, which is comprised of 368 inbred lines and planted across seven environments...
October 21, 2016: BMC Plant Biology
Si Wu, Saleh Alseekh, Álvaro Cuadros-Inostroza, Corina M Fusari, Marek Mutwil, Rik Kooke, Joost B Keurentjes, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman
Plant primary metabolism is a highly coordinated, central, and complex network of biochemical processes regulated at both the genetic and post-translational levels. The genetic basis of this network can be explored by analyzing the metabolic composition of genetically diverse genotypes in a given plant species. Here, we report an integrative strategy combining quantitative genetic mapping and metabolite‒transcript correlation networks to identify functional associations between genes and primary metabolites in Arabidopsis thaliana...
October 2016: PLoS Genetics
Jiafa Chen, Rosemary Shrestha, Junqiang Ding, Hongjian Zheng, Chunhua Mu, Jianyu Wu, George Mahuku
Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance...
October 14, 2016: G3: Genes—Genomes—Genetics
Anca Macovei, Andrea Pagano, Paola Leonetti, Daniela Carbonera, Alma Balestrazzi, Susana S Araújo
The pre-germinative metabolism is among the most fascinating aspects of seed biology. The early seed germination phase, or pre-germination, is characterized by rapid water uptake (imbibition), which directs a series of dynamic biochemical events. Among those are enzyme activation, DNA damage and repair, and use of reserve storage compounds, such as lipids, carbohydrates and proteins. Industrial seedling production and intensive agricultural production systems require seed stocks with high rate of synchronized germination and low dormancy...
October 11, 2016: Plant Cell Reports
Pieter Clauw, Frederik Coppens, Arthur Korte, Dorota Herman, Bram Slabbinck, Stijn Dhondt, Twiggy Van Daele, Liesbeth De Milde, Mattias Vermeersch, Katrien Maleux, Steven Maere, Nathalie Gonzalez, Dirk Inzé
Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under non-lethal drought conditions is lacking. Recent advances in genomics, phenomics and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves...
October 11, 2016: Plant Cell
Wei Chen, Wensheng Wang, Meng Peng, Liang Gong, Yanqiang Gao, Jian Wan, Shouchuang Wang, Lei Shi, Bin Zhou, Zongmei Li, Xiaoxi Peng, Chenkun Yang, Lianghuan Qu, Xianqing Liu, Jie Luo
The plant metabolome is characterized by extensive diversity and is often regarded as a bridge between genome and phenome. Here we report metabolic and phenotypic genome-wide studies (mGWAS and pGWAS) in rice grain that, in addition to previous metabolic GWAS in rice leaf and maize kernel, show both distinct and overlapping aspects of genetic control of metabolism within and between species. We identify new candidate genes potentially influencing important metabolic and/or morphological traits. We show that the differential genetic architecture of rice metabolism between different tissues is in part determined by tissue specific expression...
October 4, 2016: Nature Communications
Armin Scheben, Jacqueline Batley, David Edwards
In the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practise. New methods allowing rapid, high-throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping by sequencing (GBS) methods include over a dozen reduced representation sequencing (RRS) approaches and at least four whole genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best-suited method seem a daunting task...
October 3, 2016: Plant Biotechnology Journal
Tepsuda Rungrat, Mariam Awlia, Tim Brown, Riyan Cheng, Xavier Sirault, Jiri Fajkus, Martin Trtilek, Bob Furbank, Murray Badger, Mark Tester, Barry J Pogson, Justin O Borevitz, Pip Wilson
Monitoring the photosynthetic performance of plants is a major key to understanding how plants adapt to their growth conditions. Stress tolerance traits have a high genetic complexity as plants are constantly, and unavoidably, exposed to numerous stress factors, which limits their growth rates in the natural environment. Arabidopsis thaliana, with its broad genetic diversity and wide climatic range, has been shown to successfully adapt to stressful conditions to ensure the completion of its life cycle. As a result, A...
2016: Arabidopsis Book
Annett Richter, Claudia Schaff, Zhiwu Zhang, Alexander E Lipka, Feng Tian, Tobias G Köllner, Christiane Schnee, Susanne Preiss, Sandra Irmisch, Georg Jander, Wilhelm Boland, Jonathan Gershenzon, Edward S Buckler, Jorg Degenhardt
Plant volatiles not only have multiple defense functions against herbivores, fungi, and bacteria, but also have been implicated in signaling within the plant and towards other organisms. Elucidating the function of individual plant volatiles will require more knowledge of their biosynthesis and regulation in response to external stimuli. By exploiting the variation of herbivore-induced volatiles among 26 maize (Zea mays) inbred lines, we conducted a nested association mapping (NAM) and genome-wide association study (GWAS) to identify a set of quantitative trait loci (QTLs) for investigating the pathways of volatile terpene production...
September 23, 2016: Plant Cell
Annette M Fahrenkrog, Leandro G Neves, Márcio F R Resende, Ana I Vazquez, Gustavo de Los Campos, Christopher Dervinis, Robert Sykes, Mark Davis, Ruth Davenport, William B Barbazuk, Matias Kirst
Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals...
September 6, 2016: New Phytologist
Fabian Grandke, Priyanka Singh, Henri C M Heuven, Jorn R de Haan, Dirk Metzler
BACKGROUND: Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing technologies. While genotype classification is an established noise reduction step in diploids, it gains complexity with increasing ploidy levels. Eventually, the errors produced by misclassifications exceed the benefits of genotype classes...
2016: BMC Genomics
Chengming Sun, Benqi Wang, Lei Yan, Kaining Hu, Sheng Liu, Yongming Zhou, Chunyun Guan, Zhenqian Zhang, Jiana Li, Jiefu Zhang, Song Chen, Jing Wen, Chaozhi Ma, Jinxing Tu, Jinxiong Shen, Tingdong Fu, Bin Yi
Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5...
2016: Frontiers in Plant Science
Matthew W Horton, Glenda Willems, Eriko Sasaki, Maarten Koornneef, Magnus Nordborg
The capacity to tolerate freezing temperatures limits the geographical distribution of many plants, including several species of agricultural importance. However, the genes involved in freezing tolerance remain largely unknown. Here, we describe the variation in constitutive freezing tolerance that occurs among worldwide accessions of Arabidopsis thaliana. We found that although plants from high latitudes tend to be more freezing tolerant than plants from low latitudes, the environmental factors that shape cold adaptation differ across the species range...
November 2016: Plant, Cell & Environment
Kun Li, Hongwu Wang, Xiaojiao Hu, Zhifang Liu, Yujin Wu, Changling Huang
Lignin, cellulose and hemicellulose are the three main components of the plant cell wall and can impact stalk quality by affecting cell wall structure and strength. In this study, we evaluated the lignin (LIG), cellulose (CEL) and hemicellulose (HC) contents in maize using an association mapping panel that included 368 inbred lines in seven environments. A genome-wide association study using approximately 0.56 million SNPs with a minor allele frequency of 0.05 identified 22, 18 and 24 loci significantly associated with LIG, CEL and HC at P < 1...
2016: PloS One
Marta Francisco, Bindu Joseph, Hart Caligagan, Baohua Li, Jason A Corwin, Catherine Lin, Rachel E Kerwin, Meike Burow, Daniel J Kliebenstein
A key limitation in modern biology is the ability to rapidly identify genes underlying newly identified complex phenotypes. Genome wide association studies (GWAS) have become an increasingly important approach for dissecting natural variation by associating phenotypes with genotypes at a genome wide level. Recent work is showing that the Arabidopsis thaliana defense metabolite, allyl glucosinolate (GSL), may provide direct feedback regulation, linking defense metabolism outputs to the growth, and defense responses of the plant...
2016: Frontiers in Plant Science
Renée Prins, Susanne Dreisigacker, Zakkie Pretorius, Hester van Schalkwyk, Elsabet Wessels, Corneli Smit, Cornel Bender, Davinder Singh, Lesley A Boyd
Following the emergence of the Ug99 lineage of Puccinia graminis f. sp. tritici (Pgt) a collective international effort has been undertaken to identify new sources of wheat stem rust resistance effective against these races. Analyses were undertaken in a collection of wheat genotypes gathered from across Africa to identify stem rust resistance effective against the Pgt races found in Eastern and Southern Africa. The African wheat collection consisted of historic genotypes collected in Kenya, South Africa, Ethiopia, Sudan, Zambia, Morocco, and Tunisia, and current South African breeding lines...
2016: Frontiers in Plant Science
Benedikt Digel, Elahe Tavakol, Gabriele Verderio, Alessandro Tondelli, Xin Xu, Luigi Cattivelli, Laura Rossini, Maria von Korff
Leaf size is a major determinant of plant photosynthetic activity and biomass; however, it is poorly understood how leaf size is genetically controlled in cereal crop plants like barley (Hordeum vulgare). We conducted a genome-wide association scan for flowering time, leaf width, and leaf length in a diverse panel of European winter cultivars grown in the field and genotyped with a single-nucleotide polymorphism array. The genome-wide association scan identified PHOTOPERIOD-H1 (Ppd-H1) as a candidate gene underlying the major quantitative trait loci for flowering time and leaf size in the barley population...
September 2016: Plant Physiology
Ahmad M Alqudah, Ravi Koppolu, Gizaw M Wolde, Andreas Graner, Thorsten Schnurbusch
Plant stature in temperate cereals is predominantly controlled by tillering and plant height as complex agronomic traits, representing important determinants of grain yield. This study was designed to reveal the genetic basis of tillering at five developmental stages and plant height at harvest in 218 worldwide spring barley (Hordeum vulgare L.) accessions under greenhouse conditions. The accessions were structured based on row-type classes [two- vs. six-rowed] and photoperiod response [photoperiod-sensitive (Ppd-H1) vs...
2016: Frontiers in Genetics
Yuanyuan Gao, Zhaohui Liu, Jonathon Richards, Robert Saxon Brueggeman, Xuehui Li, Richard Peter Oliver, Bruce A McDonald, Justin D Faris, Timothy L Friesen
Parastagonospora nodorum is a necrotrophic fungal pathogen causing Septoria nodorum blotch (SNB) on wheat. We have identified nine necrotrophic effector-host dominant sensitivity gene interactions, and we have cloned three of the necrotrophic effector (NE) genes, including SnToxA, SnTox1 and SnTox3. Because sexual populations of P. nodorum are difficult to develop under lab conditions, genome wide association study (GWAS) is the best population genomic approach to identify genomic regions associated with traits using natural populations...
July 20, 2016: Phytopathology
Qiang Zhang, Tianqing Zheng, Long Hoang, Chunchao Wang, Nafisah, Charles Joseph, Wenzhong Zhang, Jianlong Xu, Zhikang Li
The rolled leaf trait, long considered to be a key component of plant architecture, represents an important target trait for improving plant architecture at the population level. We therefore performed linkage mapping using a set of 262 highly variable RILs from two rice cultivars (Minghui 63 and 02428) with minor differences in leaf rolling index (LRI) in conjunction with GWAS mapping of a random subset of the 1127 germplasms from the 3K Rice Genomes Project (3K Rice). A total of seven main-effect loci were found to underlie the transgressive segregation of progenies from parents with minor differences in LRI...
2016: PloS One
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