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Plant association mapping

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https://www.readbyqxmd.com/read/28339482/a-genome-wide-identification-and-analysis-of-the-dyw-deaminase-genes-in-the-pentatricopeptide-repeat-gene-family-in-cotton-gossypium-spp
#1
Bingbing Zhang, Guoyuan Liu, Xue Li, Liping Guo, Xuexian Zhang, Tingxiang Qi, Hailin Wang, Huini Tang, Xiuqin Qiao, Jinfa Zhang, Chaozhu Xing, Jianyong Wu
The RNA editing occurring in plant organellar genomes mainly involves the change of cytidine to uridine. This process involves a deamination reaction, with cytidine deaminase as the catalyst. Pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain are reportedly associated with cytidine deamination, similar to members of the deaminase superfamily. PPR genes are involved in many cellular functions and biological processes including fertility restoration to cytoplasmic male sterility (CMS) in plants...
2017: PloS One
https://www.readbyqxmd.com/read/28338805/deciphering-the-genetic-control-of-fruit-texture-in-apple-by-multiple-family-based-analysis-and-genome-wide-association
#2
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...
February 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28330322/de-novo-transcriptome-sequencing-in-monsonia-burkeana-revealed-putative-genes-for-key-metabolic-pathways-involved-in-tea-quality-and-medicinal-value
#3
Adugna A Woldesemayat, Khayalethu Ntushelo, David M Modise
Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28315926/dissection-of-a-major-qtl-qhir1-conferring-maternal-haploid-induction-ability-in-maize
#4
Sudha K Nair, Willem Molenaar, Albrecht E Melchinger, Prasanna M Boddupalli, Leocadio Martinez, Luis Antonio Lopez, Vijay Chaikam
Among the qhir11 and qhir12 sub-regions of a major QTL qhir1, only qhir11 has significant effect on maternal haploid induction, segregation distortion and kernel abortion. In vivo haploid induction in maize can be triggered in high frequencies by pollination with special genetic stocks called haploid inducers. Several genetic studies with segregating populations from non-inducer x inducer crosses identified a major QTL, qhir1, on chromosome 1.04 contributing to in vivo haploid induction. A recent Genome Wide Association Study using 51 inducers and 1482 non-inducers also identified two sub-regions within the qhir1 QTL region, named qhir11 and qhir12; qhir12 was proposed to be mandatory for haploid induction because the haplotype of qhir11 was also present in some non-inducers and putative candidate genes coding for DNA and amino acid binding proteins were identified in the qhir12 region...
March 18, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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
#5
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/28295033/myosin-xi-is-associated-with-fitness-and-adaptation-to-aridity-in-wild-pearl-millet
#6
I S Ousseini, Y Bakasso, N A Kane, M Couderc, L Zekraoui, C Mariac, D Manicacci, B Rhoné, A Barnaud, C Berthouly-Salazar, A Assoumane, D Moussa, T Moussa, Y Vigouroux
Phenotypic changes in plants can be observed along many environmental gradients and are determined by both environmental and genetic factors. The identification of alleles associated with phenotypic variations is a rapidly developing area of research. We studied the genetic basis of phenotypic variations in 11 populations of wild pearl millet (Pennisetum glaucum) on two North-South aridity gradients, one in Niger and one in Mali. Most of the 11 phenotypic traits assessed in a common garden experiment varied between the populations studied...
March 15, 2017: Heredity
https://www.readbyqxmd.com/read/28282528/spatio-temporal-dynamics-in-global-rice-gene-expression-oryza-sativa%C3%A2-l-in-response-to-high-ammonium-stress
#7
Li Sun, Dongwei Di, Guangjie Li, Herbert J Kronzucker, Weiming Shi
Ammonium (NH4(+)) is the predominant nitrogen (N) source in many natural and agricultural ecosystems, including flooded rice fields. While rice is known as an NH4(+)-tolerant species, it nevertheless suffers NH4(+) toxicity at elevated soil concentrations. NH4(+) excess rapidly leads to the disturbance of various physiological processes that ultimately inhibit shoot and root growth. However, the global transcriptomic response to NH4(+) stress in rice has not been examined. In this study, we mapped the spatio-temporal specificity of gene expression profiles in rice under excess NH4(+) and the changes in gene expression in root and shoot at various time points by RNA-Seq (Quantification) using Illumina HiSeqTM 2000...
February 22, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28282385/genetic-architecture-of-cold-tolerance-in-rice-oryza-sativa-determined-through-high-resolution-genome-wide-analysis
#8
Ehsan Shakiba, Jeremy D Edwards, Farman Jodari, Sara E Duke, Angela M Baldo, Pavel Korniliev, Susan R McCouch, Georgia C Eizenga
Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers...
2017: PloS One
https://www.readbyqxmd.com/read/28281636/a-high-density-snp-genetic-map-consisting-of-a-complete-set-of-homologous-groups-in-autohexaploid-sweetpotato-ipomoea-batatas
#9
Kenta Shirasawa, Masaru Tanaka, Yasuhiro Takahata, Daifu Ma, Qinghe Cao, Qingchang Liu, Hong Zhai, Sang-Soo Kwak, Jae Cheol Jeong, Ung-Han Yoon, Hyeong-Un Lee, Hideki Hirakawa, Sachiko Isobe
Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28270831/genomic-prediction-of-genotypic-effects-with-epistasis-and-environment-interactions-for-yield-related-traits-of-rapeseed-brassica-napus-l
#10
Xiang Luo, Yi Ding, Linzhong Zhang, Yao Yue, John H Snyder, Chaozhi Ma, Jun Zhu
Oilseed rape (Brassica napus) is an economically important oil crop, yet the genetic architecture of its complex traits remain largely unknown. Here, genome-wide association study was conducted for eight yield-related traits to dissect the genetic architecture of additive, dominance, epistasis, and their environment interaction. Additionally, the optimal genotype combination and the breeding value of superior line, superior hybrid and existing best line in mapping population were predicted for each trait in two environments based on the predicted genotypic effects...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28258751/assessing-top-and-subsoil-organic-carbon-stocks-of-low-input-high-diversity-systems-using-soil-and-vegetation-characteristics
#11
Sam Ottoy, Koenraad Van Meerbeek, Anicet Sindayihebura, Martin Hermy, Jos Van Orshoven
The soil organic carbon (SOC) stock is an important indicator in ecosystem service assessments. Even though a considerable fraction of the total stock is stored in the subsoil, current assessments often consider the topsoil only. Furthermore, mapping efforts are hampered by the limited spatial density of these topsoil measurements. The aim of this study was to assess the SOC stock in the upper 100cm of soil in 30,556ha of Low-Input High-Diversity systems, such as nature reserves, in Flanders (Belgium) and compare this estimate with the stock found in the topsoil (upper 15cm)...
March 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28257442/genotyping-by-sequencing-markers-facilitate-the-identification-of-quantitative-trait-loci-controlling-resistance-to-penicillium-expansum-in-malus-sieversii
#12
John L Norelli, Michael Wisniewski, Gennaro Fazio, Erik Burchard, Benjamin Gutierrez, Elena Levin, Samir Droby
Blue mold caused by Penicillium expansum is the most important postharvest disease of apple worldwide and results in significant financial losses. There are no defined sources of resistance to blue mold in domesticated apple. However, resistance has been described in wild Malus sieversii accessions, including plant introduction (PI)613981. The objective of the present study was to identify the genetic loci controlling resistance to blue mold in this accession. We describe the first quantitative trait loci (QTL) reported in the Rosaceae tribe Maleae conditioning resistance to P...
2017: PloS One
https://www.readbyqxmd.com/read/28252189/quantitative-trait-loci-controlling-leaf-venation-in-arabidopsis
#13
Louai Rishmawi, Jonas Bühler, Benjamin Jaegle, Martin Hülskamp, Maarten Koornneef
Leaf veins provide the mechanical support and are responsible for the transport of nutrients and water to the plant. High vein density is a prerequisite for plants to have C4 photosynthesis. We investigated the genetic variation and genetic architecture of leaf venation traits within the species Arabidopsis thaliana using natural variation. Leaf venation traits, including leaf vein density (LVD) were analyzed in 66 worldwide accessions and 399 lines of the multi-parent advanced generation intercross (MAGIC) population...
March 2, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28250803/medical-subject-heading-mesh-annotations-illuminate-maize-genetics-and-evolution
#14
Timothy M Beissinger, Gota Morota
BACKGROUND: High-density marker panels and/or whole-genome sequencing, coupled with advanced phenotyping pipelines and sophisticated statistical methods, have dramatically increased our ability to generate lists of candidate genes or regions that are putatively associated with phenotypes or processes of interest. However, the speed with which we can validate genes, or even make reasonable biological interpretations about the principles underlying them, has not kept pace. A promising approach that runs parallel to explicitly validating individual genes is analyzing a set of genes together and assessing the biological similarities among them...
2017: Plant Methods
https://www.readbyqxmd.com/read/28244240/mst50-is-involved-in-multiple-map-kinase-signaling-pathways-in-magnaporthe-oryzae
#15
Guotian Li, Xue Zhang, Huan Tian, Yoon-E Choi, W Andy Tao, Jin-Rong Xu
Appressorium formation plays a critical role in Magnaporthe oryzae. Mst50 is an adapter protein of the Mst11-Mst7-Pmk1 cascade that is essential for appressorium formation. To further characterize its functions, affinity purification was used to identify Mst50-interacting proteins (MIPs) in this study. Two of the MIPs are Mst11 and Mst7 that are known to interact with Mst50 for Pmk1 activation. Surprisingly, two other MIPs are Mck1 and Mkk2 that are the upstream kinases of the Mps1 pathway. Domain deletion analysis showed that the sterile alpha-motif of Mst50 but not the Ras-association domain was important for its interaction with Mck1 and responses to cell wall and oxidative stresses...
February 28, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28241374/linking-above-and-belowground-traits-to-soil-and-climate-variables-an-integrated-database-on-china-s-grassland-species
#16
Yan Geng, Wenhong Ma, Liang Wang, Frank Baumann, Peter Kühn, Thomas Scholten, Jin-Sheng He
Knowledge of plant functional traits and trait-environment interactions is important for characterizing species strategies and understanding ecological processes. However, comprehensive field data on both above- and belowground traits, together with their environmental variables are scarce. Biome-scale studies are particularly lacking. Here we present two large-scale datasets that include functional traits of leaves and fine roots and their corresponding soil and climatic variables in China's grasslands. Leaf, fine root and soil samples were collected in three biogeographic regions: temperate grassland on the Inner Mongolia Plateau, alpine grassland on the Tibetan Plateau, and mountain grassland in the Xinjiang mountain areas...
February 27, 2017: Ecology
https://www.readbyqxmd.com/read/28241006/identification-and-validation-of-single-nucleotide-polymorphic-markers-linked-to-ug99-stem-rust-resistance-in-spring-wheat
#17
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/28238159/analyses-of-pea-necrotic-yellow-dwarf-virus-encoded-proteins
#18
Björn Krenz, Ingrid Schießl, Eva Greiner, Susanna Krapp
Pea necrotic yellow dwarf virus (PNYDV) is a multipartite, circular, single-stranded DNA plant virus. PNYDV encodes eight proteins and the function of three of which remains unknown-U1, U2, and U4. PNYDV proteins cellular localization was analyzed by GFP tagging and bimolecular fluorescence complementation (BiFC) studies. The interactions of all eight PNYDV proteins were tested pairwise in planta (36 combinations in total). Seven interactions were identified and two (M-Rep with CP and MP with U4) were characterized further...
February 25, 2017: Virus Genes
https://www.readbyqxmd.com/read/28231290/mapping-the-sensory-perception-of-apple-using-descriptive-sensory-evaluation-in-a-genome-wide-association-study
#19
Beatrice Amyotte, Amy J Bowen, Travis Banks, Istvan Rajcan, Daryl J Somers
Breeding apples is a long-term endeavour and it is imperative that new cultivars are selected to have outstanding consumer appeal. This study has taken the approach of merging sensory science with genome wide association analyses in order to map the human perception of apple flavour and texture onto the apple genome. The goal was to identify genomic associations that could be used in breeding apples for improved fruit quality. A collection of 85 apple cultivars was examined over two years through descriptive sensory evaluation by a trained sensory panel...
2017: PloS One
https://www.readbyqxmd.com/read/28228093/comparative-profiling-of-hepatopancreas-transcriptomes-in-satiated-and-starving-pomacea-canaliculata
#20
Lei Yang, Tian-Yin Cheng, Fei-Yan Zhao
BACKGROUND: Although Pomacea canaliculata is native to South and Central America, it has become one of the most abundant invasive species worldwide and causes extensive damage to agriculture and horticulture. Conventional physical and chemical techniques have been used to eliminate P. canaliculata, but the effects are not ideal. Therefore, it is important to devise a new method based on a greater understanding of the biology of P. canaliculata. However, the molecular mechanisms underlying digestion and absorption in P...
February 22, 2017: BMC Genetics
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