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Plant Genome

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https://read.qxmd.com/read/30512048/prospects-and-challenges-of-applied-genomic-selection-a-new-paradigm-in-breeding-for-grain-yield-in-bread-wheat
#1
Philomin Juliana, Ravi P Singh, Jesse Poland, Suchismita Mondal, José Crossa, Osval A Montesinos-López, Susanne Dreisigacker, Paulino Pérez-Rodríguez, Julio Huerta-Espino, Leonardo Crespo-Herrera, Velu Govindan
Genomic selection (GS) has been promising for increasing genetic gains in several species. Therefore, we evaluated the potential integration of GS for grain yield (GY) in bread wheat ( L.) in CIMMYT's elite yield trial nurseries. We observed that the genomic prediction accuracies within nurseries (0.44 and 0.35) were substantially higher than across-nursery accuracies (0.15 and 0.05) for GY evaluated in the bed and flat planting systems, respectively. The accuracies from using only a subset of 251 genotyping-by-sequencing markers were comparable to the accuracies using all 2038 markers...
November 2018: Plant Genome
https://read.qxmd.com/read/30512047/an-r-package-for-multitrait-and-multienvironment-data-with-the-item-based-collaborative-filtering-algorithm
#2
Osval A Montesinos-López, Francisco Javier Luna-Vázquez, Abelardo Montesinos-López, Philomin Juliana, Ravi Singh, José Crossa
The Item-Based Collaborative Filtering for Multitrait and Multienvironment Data (IBCF.MTME) package was developed to implement the item-based collaborative filtering (IBCF) algorithm for continuous phenotypic data in the context of plant breeding where data are collected for various traits and environments. The main difference between this package and the other available packages that can implement IBCF is that this one was developed for continuous phenotypic data, which cannot be implemented in the current packages because they can implement IBCF only for binary and ordinary phenotypes...
November 2018: Plant Genome
https://read.qxmd.com/read/30512046/genome-wide-association-mapping-of-host-plant-resistance-to-soybean-aphid
#3
Anthony A Hanson, Aaron J Lorenz, Louis S Hesler, Siddhi J Bhusal, Raman Bansal, Andy P Michel, Guo-Liang Jiang, Robert L Koch
Soybean aphid [ Matsumura (Hemiptera: Aphididae)] is the most damaging insect pest of soybean [ (L.) Merr.] in the Upper Midwest of the United States and is primarily controlled by insecticides. Soybean aphid resistance (i.e., genes) has been documented in some soybean accessions but more sources of resistance are needed. Incorporation of the resistance into marketed varieties has also been slow. Genome-wide association mapping can aid in identifying resistant accessions by correlating phenotypic data with single nucleotide polymorphisms (SNPs) across a genome...
November 2018: Plant Genome
https://read.qxmd.com/read/30512045/identification-and-mapping-of-late-blight-resistance-quantitative-trait-loci-in-tomato-accession-pi-163245
#4
Erik W Ohlson, Hamid Ashrafi, Majid R Foolad
Late blight (LB), caused by the oomycete (Mont.) de Bary, is one of the most devastating diseases of tomato ( L.) and potato ( tuberosum L. worldwide. The importance of LB on tomato has increased due to the occurrence of aggressive and fungicide-resistant clonal lineages of . Consequently, identification and characterization of new sources of genetic resistance to LB has become a priority in tomato breeding. Previously, we reported accession PI 163245 as a promising source of highly heritable LB resistance for tomato breeding...
November 2018: Plant Genome
https://read.qxmd.com/read/30512044/combining-three-mapping-strategies-to-reveal-quantitative-trait-loci-and-candidate-genes-for-maize-ear-length
#5
Bo Zhou, Zijian Zhou, Junqiang Ding, Xuecai Zhang, Cong Mu, Yabin Wu, Jingyang Gao, Yunxia Song, Shiwei Wang, Jinliang Ma, Xiantang Li, Ruixia Wang, Zongliang Xia, Jiafa Chen, Jianyu Wu
Ear length (EL) is an important trait in maize ( L.) because it is positively correlated with grain yield. To understand the genetic basis of natural EL variation, a F, a four-way cross and a genome-wide association study (GWAS) population were used to identify the quantitative trait loci (QTLs) and candidate EL genes. Linkage mapping identified 14 QTLs in two types of populations from multiple environments. Six of them were located in three common genomic regions considered "stable QTLs". Candidate genes for the three stable QTLs were identified by the GWAS results...
November 2018: Plant Genome
https://read.qxmd.com/read/30512043/development-and-application-of-high-density-axiom-cajanus-snp-array-with-56k-snps-to-understand-the-genome-architecture-of-released-cultivars-and-founder-genotypes
#6
Rachit K Saxena, Abhishek Rathore, Abhishek Bohra, Pooja Yadav, Roma Rani Das, Aamir W Khan, Vikas K Singh, Annapurna Chitikineni, Indra P Singh, C V Sameer Kumar, K B Saxena, Rajeev K Varshney
As one of the major outputs of next-generation sequencing (NGS), a large number of genome-wide single-nucleotide polymorphisms (SNPs) have been developed in pigeonpea [ (L.) Huth.]. However, SNPs require a genotyping platform or assay to be used in different evolutionary studies or in crop improvement programs. Therefore, we developed an Axiom SNP array with 56K SNPs uniformly distributed across the genome and assessed its utility in a genetic diversity study. From the whole-genome resequencing (WGRS) data on 104 pigeonpea lines, ∼2 million sequence variations (SNPs and insertion-deletions [InDels]) were identified, from which a subset of 56,512 unique and informative sequence variations were selected to develop the array...
November 2018: Plant Genome
https://read.qxmd.com/read/30512042/genome-wide-characterization-and-expression-analysis-of-sugar-transporter-family-genes-in-woodland-strawberry
#7
Songtao Jiu, Muhammad Salman Haider, Mahantesh M Kurjogi, Kekun Zhang, Xudong Zhu, Jinggui Fang
In higher plants, sugars are nutrients and important signal molecules. Sugar transporters (STs) facilitate sugar transport across membranes and are associated with loading and unloading of the conducting complex. Strawberry ( Duchesne ex Rozier) is one of the most economically important and widely cultivated fruit crop and a model plant among fleshy fruits worldwide. In this study, 66 woodland strawberry ( L.) ST (FvST) genes were identified and further classified into eight distinct subfamilies in the woodland strawberry genome based on the phylogenetic analysis...
November 2018: Plant Genome
https://read.qxmd.com/read/30512041/research-highlights
#8
(no author information available yet)
No abstract text is available yet for this article.
November 2018: Plant Genome
https://read.qxmd.com/read/30512040/transcriptome-analysis-provides-insights-into-gingerol-biosynthesis-in-ginger-zingiber-officinale
#9
Yusong Jiang, Mengjun Huang, Michael Wisniewski, Honglei Li, Meixia Zhang, Xiang Tao, Yiqing Liu, Yong Zou
Ginger ( Roscoe), a perennial herb, is one of the most economically valuable plants in the Zingiberaceae family. Gingerol, as the major constituents of ginger essential oil, contributes to the unique flavor and pharmaceutical value of ginger. However, the pathway of gingerol biosynthesis has not been verified and described in ginger to help understand the biosynthesis of secondary metabolites in nonmodel species. In this study, the concentrations of gingerols were quantified at different stages of rhizome development and in different tissues...
November 2018: Plant Genome
https://read.qxmd.com/read/30512039/evaluation-of-genetic-variation-among-sorghum-varieties-from-southwest-china-via-genome-resequencing
#10
Songxian Yan, Li Wang, Liang Zhao, Heyu Wang, Diqiang Wang
Little is known regarding genomic variation among glutinous sorghum [ (L.) Moench] varieties grown in southwest China, which are primarily used to brew the popular Jiang-flavor liquor. This study evaluated genomic variation among six representative sorghum accessions via whole-genome resequencing. The evaluation revealed 2365,363 single-nucleotide polymorphisms (SNPs), 394,365 insertions and deletions, and 47,567 copy number variations among the six genomes. Chromosomes 5 and 10 showed relatively high SNP densities, whereas whole-genome diversity in this population was low...
November 2018: Plant Genome
https://read.qxmd.com/read/30512038/understanding-the-complexity-of-cold-tolerance-in-white-clover-using-temperature-gradient-locations-and-a-gwas-approach
#11
Luis Inostroza, Mehul Bhakta, Hernán Acuña, Catalina Vásquez, Joel Ibáñez, Gerardo Tapia, Wenbin Mei, Matias Kirst, Marcio Resende, Patricio Munoz
White clover ( L.) is the most important grazing perennial forage legume in temperate climates. However, its limited capacity to survive and restore growth after low temperatures during winter constrains the productivity and wide adoption of the crop. Despite the importance of cold tolerance for white clover cultivar development, the genetic basis of this trait remains largely unknown. Hence, in this study, we performed the first genome-wide association study (GWAS) analyses in white clover to identify quantitative trait loci (QTL) for cold-tolerance-related traits...
November 2018: Plant Genome
https://read.qxmd.com/read/30512037/domestication-of-temperate-and-coastal-hybrids-with-distinct-ancestral-gene-selection-in-octoploid-strawberry
#12
Michael A Hardigan, Thomas J Poorten, Charlotte B Acharya, Glenn S Cole, Kim E Hummer, Nahla Bassil, Patrick P Edger, Steven J Knapp
Garden strawberry ( × Duchesne ex Rozier) arose from spontaneous hybridization of distinct octoploid species 300 yr ago. Since its discovery in the 1700s, migration and selection restructured the genetic diversity of early hybrids to produce elite fruit-bearing groups. Breeders' understanding of the genetic architecture of domesticated populations is incomplete. To resolve the impacts of domestication on strawberry genetic diversity, we analyzed genome-wide DNA profiles of 1300 octoploid individuals (1814-present), including wild species, historic varieties, and the University of California germplasm collection...
November 2018: Plant Genome
https://read.qxmd.com/read/30512036/-tripsacum-de-novo-transcriptome-assemblies-reveal-parallel-gene-evolution-with-maize-after-ancient-polyploidy
#13
Christine M Gault, Karl A Kremling, Edward S Buckler
Plant genomes reduce in size following a whole-genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize ( L.) and its sister genus, , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for exist, it is unknown whether grasses and maize have maintained a similar set of genes that have resisted decay into pseudogenes. Here we present high-quality de novo transcriptome assemblies for two species: (L...
November 2018: Plant Genome
https://read.qxmd.com/read/30512035/genome-wide-association-study-using-historical-breeding-populations-discovers-genomic-regions-involved-in-high-quality-rice
#14
Gastón Quero, Lucía Gutiérrez, Eliana Monteverde, Pedro Blanco, Fernando Pérez de Vida, Juan Rosas, Schubert Fernández, Silvia Garaycochea, Susan McCouch, Natalia Berberian, Sebastián Simondi, Victoria Bonnecarrère
Rice ( L.) is one of the most important staple food crops in the world; however, there has recently been a shift in consumer demand for higher grain quality. Therefore, understanding the genetic architecture of grain quality has become a key objective of rice breeding programs. Genome-wide association studies (GWAS) using large diversity panels have successfully identified genomic regions associated with complex traits in diverse crop species. Our main objective was to identify genomic regions associated with grain quality and to identify and characterize favorable haplotypes for selection...
November 2018: Plant Genome
https://read.qxmd.com/read/30512034/structural-variation-functional-differentiation-and-activity-correlation-of-the-cytochrome-p450-gene-superfamily-revealed-in-ginseng
#15
Yi Wang, Xiangyu Li, Yanping Lin, Yanfang Wang, Kangyu Wang, Chunyu Sun, Tiancheng Lu, Meiping Zhang
Ginseng ( C.A. Mey.) is one of the most important medicinal herbs for human health and medicine, for which ginsenosides are the major bioactive components. The cytochrome P450 genes, , form a large gene superfamily; however, only three genes have been identified from ginseng and shown to be involved in ginsenoside biosynthesis, indicating the importance of the gene superfamily in the process. Here we report genome-wide identification and systems analysis of the genes in ginseng, defined as genes. We identified 414 genes, including the three published genes...
November 2018: Plant Genome
https://read.qxmd.com/read/30512033/genomic-analysis-and-prediction-within-a-us-public-collaborative-winter-wheat-regional-testing-nursery
#16
Trevor W Rife, Robert A Graybosch, Jesse A Poland
The development of inexpensive, whole-genome profiling enables a transition to allele-based breeding using genomic prediction models. These models consider alleles shared between lines to predict phenotypes and select new lines based on estimated breeding values. This approach can leverage highly unbalanced datasets that are common to breeding programs. The Southern Regional Performance Nursery (SRPN) is a public nursery established by the USDA-ARS in 1931 to characterize performance and quality of near-release wheat ( L...
November 2018: Plant Genome
https://read.qxmd.com/read/30512032/candidate-variants-for-additive-and-interactive-effects-on-bioenergy-traits-in-switchgrass-panicum-virgatum-l-identified-by-genome-wide-association-analyses
#17
Guillaume P Ramstein, Joseph Evans, Aruna Nandety, Malay C Saha, E Charles Brummer, Shawn M Kaeppler, C Robin Buell, Michael D Casler
Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes...
November 2018: Plant Genome
https://read.qxmd.com/read/30512031/transcriptome-analysis-and-functional-identification-of-xa13-and-pi-ta-orthologs-in-oryza-granulata
#18
Rui Yang, Jing Li, Hui Zhang, Fei Yang, Zhigang Wu, Xiaoxuan Zhuo, Xingyu An, Zaiquan Cheng, Qianchun Zeng, Qiong Luo
Nees & Arn. ex Watt, a perennial wild rice species with a GG genome, preserves many important genes for cultivated rice ( L.) improvement. At present, however, no genetic resource is available for studying . Here, we report 91,562 high-quality transcripts of assembled de novo. Moreover, comparative transcriptome analysis revealed that 1311 single-copy orthologous pairs shared by and (Zoll. & Moritzi) Baill. that may have undergone adaptive evolution. We performed an analysis of the genes potentially involved in plant-pathogen interactions to explore the molecular basis of disease resistance, and isolated the full-length cDNAs of () and () orthologs from ...
November 2018: Plant Genome
https://read.qxmd.com/read/30025030/resequencing-of-common-bean-identifies-regions-of-inter-gene-pool-introgression-and-provides-comprehensive-resources-for-molecular-breeding
#19
(no author information available yet)
No abstract text is available yet for this article.
July 2018: Plant Genome
https://read.qxmd.com/read/30025029/resequencing-of-common-bean-identifies-regions-of-inter-gene-pool-introgression-and-provides-comprehensive-resources-for-molecular-breeding
#20
Juan David Lobaton, Tamara Miller, Juanita Gil, Daniel Ariza, Juan Fernando de la Hoz, Alvaro Soler, Steve Beebe, Jorge Duitama, Paul Gepts, Bodo Raatz
Common bean ( L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to , (A...
July 2018: Plant Genome
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