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Plant association mapping

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
Yue Liu, Wenli Zhang, Kang Zhang, Qi You, Hengyu Yan, Yuannian Jiao, Jiming Jiang, Wenying Xu, Zhen Su
Light, as the energy source in photosynthesis, is essential for plant growth and development. Extended darkness causes dramatic gene expression changes. In this study, we applied DNase-seq (DNase I hypersensitive site sequencing) to study changes of chromatin accessibility in euchromatic and heterochromatic regions under extended darkness in Arabidopsis. We generated 27 Gb DNase-seq and 67.6 Gb RNA-seq data to investigate chromatin accessibility changes and global gene expression under extended darkness and control condition in Arabidopsis...
June 22, 2017: Scientific Reports
Tefera Tolera Angessa, Xiao-Qi Zhang, Gaofeng Zhou, Sue Broughton, Wenying Zhang, Chengdao Li
A doubled haploid (DH) population of barley (Hordeum vulgare L.) generated from salinity tolerant genotype CM72 and salinity sensitive variety Gairdner was studied for salinity stress tolerance at germination, seedling emergence and first leaf full expansion growth stages. Germination study was conducted with deionized water, 150 mM and 300 mM NaCl treatments. Seedling stage salinity tolerance was conducted with three treatments: control, 150 mM NaCl added at seedling emergence and first leaf full expansion growth stages...
2017: PloS One
Jian Song, Zhen Li, Zhangxiong Liu, Yong Guo, Li-Juan Qiu
Next-generation sequencing (NGS)-based bulked-segregant analysis (BSA) approaches have been proven successful for rapidly mapping genes in plant species. However, most such methods are based on mutants and usually only one gene controlling the mutant phenotype is identified. In this study, NGS-based BSA was employed to map simultaneously two qualitative genes controlling cotyledon color of seed in soybean. Yellow-cotyledon (YC) and green-cotyledon (GC) bulks from progenies of a biparental population (Zhonghuang 30 × Jiyu 102) were sequenced...
2017: Frontiers in Plant Science
Jonathan Corbi, Eric J Baack, Jennifer M Dechaine, Gerald Seiler, John M Burke
Crop-wild hybridization occurs in numerous plant species, and could alter the genetic structure and evolutionary dynamics of wild populations. Studying crop-derived alleles in wild populations is also relevant to assessing/mitigating the risks associated with transgene escape. To date, crop-wild hybridization has generally been examined via short-term studies, typically within a single generation, focusing on few traits or genetic markers. Little is known about patterns of selection on crop-derived alleles over multiple generations, particularly at a genome-wide scale...
June 14, 2017: Molecular Ecology
Anurag V Daware, Rishi Srivastava, Ashok K Singh, Swarup K Parida, Akhilesh K Tyagi
Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs...
2017: Frontiers in Plant Science
Jiangzhou Xia, Wenping Yuan, Ying-Ping Wang, Quanguo Zhang
Carbon allocation is one of the most important physiological processes to optimize the plant growth, which exerts a strong influence on ecosystem structure and function, with potentially large implications for the global carbon budget. However, it remains unclear how the carbon allocation pattern has changed at global scale and impacted terrestrial carbon uptake. Based on the Community Atmosphere Biosphere Land Exchange (CABLE) model, this study shows the increasing partitioning ratios to leaf and wood and reducing ratio to root globally from 1979 to 2014...
June 13, 2017: Scientific Reports
Changwei Ge, Li Wang, Weijun Ye, Liwen Wu, Yongtao Cui, Ping Chen, Jiangjie Pan, Dong Zhang, Jiang Hu, Dali Zeng, Guojun Dong, Qian Qian, Longbiao Guo, Dawei Xue
Plant leaves are a crucial organ associated closely with chloroplast development, photosynthesis rate and crop productivity. In this study, a white fine stripe leaf 1 (wfsl1) mutant was isolated and characterized from the japonica rice Zhonghua11 (ZH11) after ethyl methanesulfonate mutagenesis. The wfsl1 displayed white fine stripe leaves since tillering stage and abnormal chloroplast structure. Map-based cloning and Bioinformatic analysis indicated that WFSL1 on chromosome 1 contains an "A" to "T" substitution in protein coding region, and encodes a putative metal-dependent phosphohydrolase with HD domain at the N-terminus...
June 12, 2017: Scientific Reports
Ian P Wood, Bruce M Pearson, Enriqueta Garcia-Gutierrez, Lenka Havlickova, Zhesi He, Andrea L Harper, Ian Bancroft, Keith W Waldron
Genetic improvement of the plant cell wall has enormous potential to increase the quality of food, fibers, and fuels. However, the identification and characterization of genes involved in plant cell wall synthesis is far from complete. Association mapping is one of the few techniques that can help identify candidate genes without relying on our currently incomplete knowledge of cell wall synthesis. However, few cell wall phenotyping methodologies have proven sufficiently precise, robust, or scalable for association mapping to be conducted for specific cell wall polymers...
June 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
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
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
Chitra Raghavan, Ramil Mauleon, Vanica Lacorte, Monalisa Jubay, Hein Zaw, Justine Bonifacio, Rakesh Kumar Singh, B Emma Huang, Hei Leung
Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS)...
June 7, 2017: G3: Genes—Genomes—Genetics
Sophie Bouchet, Marcus O Olatoye, Sandeep R Marla, Ramasamy Perumal, Tesfaye Tesso, Jianming Yu, Mitch Tuinstra, Geoffrey P Morris
Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]-a widely adapted cereal crop-we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing...
June 2017: Genetics
Joanna Majka, Tomasz Książczyk, Agnieszka Kiełbowicz-Matuk, David Kopecký, Arkadiusz Kosmala
The Festuca genus is thought to be the most numerous genus of the Poaceae family. One of the most agronomically important forage grasses, Festuca pratensis Huds. is treated as a model plant to study the molecular mechanisms associated with tolerance to winter stresses, including frost. However, the precise mapping of the genes governing stress tolerance in this species is difficult as its karyotype remains unrecognized. Only two F. pratensis chromosomes with 35S and 5S rDNA sequences can be easily identified, but its remaining chromosomes have not been distinguished to date...
2017: PloS One
Y Xu, C Xu, S Xu
Genomic selection holds a great promise to accelerate plant breeding via early selection before phenotypes are measured, and it offers major advantages over marker-assisted selection for highly polygenic traits. In addition to genomic data, metabolome and transcriptome are increasingly receiving attention as new data sources for phenotype prediction. We used data available from maize as a model to compare the predictive abilities of three different omic data sources using eight representative methods for six traits...
June 7, 2017: Heredity
Claudia Bartoli, Fabrice Roux
The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars...
2017: Frontiers in Plant Science
Zhiliang Xiao, Yang Hu, Xiaoli Zhang, Yuqian Xue, Zhiyuan Fang, Limei Yang, Yangyong Zhang, Yumei Liu, Zhansheng Li, Xing Liu, Zezhou Liu, Honghao Lv, Mu Zhuang
Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage (Brassica oleracea) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2, respectively...
June 5, 2017: Genes
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
Ran Qin, Dongdong Zeng, Rong Liang, Chengcong Yang, Delara Akhter, Alamin Md, Xiaoli Jin, Chunhai Shi
A new mutant named sdl (stripe and drooping leaf) was characterized from indica cultivar Zhenong 34 by ethylmethane sulfonate (EMS) mutagenesis. The mutant sdl exhibited development defects including stripe and drooping leaf, dwarfism and deformed floral organs. The gene SDL was found allelic to RNRS1 by map-based cloning, which was homologous to Arabidopsis TSO2 encoding the small subunit of ribonucleotide reductase. The gDNA sequencing results of sdl in mutant consistently showed that there was a repetitive sequence insertion of 138-bp at the 475th bp in the exon...
May 31, 2017: Gene
Su Ryun Choi, Xiaona Yu, Vignesh Dhandapani, Xiaonan Li, Zhi Wang, Seo Yeon Lee, Sang Heon Oh, Wenxing Pang, Nirala Ramchiary, Chang Pyo Hong, Suhyoung Park, Zhongyun Piao, HyeRan Kim, Yong Pyo Lim
QTLs and candidate gene markers associated with leaf morphological and color traits were identified in two immortalized populations of Brassica rapa, which will provide genetic information for marker-assisted breeding. Brassica rapa is an important leafy vegetable consumed worldwide and morphology is a key character for its breeding. To enhance genetic control, quantitative trait loci (QTLs) for leaf color and plant architecture were identified using two immortalized populations with replications of 2 and 4 years...
June 2, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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