scholarly journals Association Analysis of Arsenic-Induced Straighthead in Rice (Oryza sativa L.) Based on the Selected Population with a Modified Model

2017 ◽  
Vol 2017 ◽  
pp. 1-6
Author(s):  
Xiaobai Li ◽  
Biaolin Hu ◽  
Xuhao Pan ◽  
Ning Zhang ◽  
Dianxing Wu
Keyword(s):  
Association Mapping ◽  
Linkage Mapping ◽  
Core Collection ◽  
Oryza Sativa L ◽  
Yield Losses ◽  
Optimal Model ◽  
Physiological Disorder ◽  
Modified Model ◽  
Genome Wide ◽  
Marker Loci

A rice physiological disorder makes mature panicle keep erect with empty grains termed as “straighthead.” Straighthead causes yield losses and is a serious threat to rice production worldwide. Here, a new study of association mapping was conducted to identify QTL involved in straighthead. A subset of 380 accessions was selected from the USDA rice core collection and genotyped with 72 genome-wide SSR markers. An optimal model implemented with principle components (PCs) was used in this association mapping. As a result, five markers were identified to be significantly associated with straighthead. Three of them, RM263, RM169, and RM224, were consistent with a previous study. Three markers, RM475, RM263, and RM19, had a resistant allele associated with a decrease in straighthead rating (straighthead rating ≤ 4.8). In contrast, the two other marker loci RM169 and RM224 had a few susceptible alleles associated with an increase in straighthead rating (straighthead rating ≥ 8.7). Interestingly, RM475 is close to QTL “qSH-2” and “AsS” with straighthead resistance, which was reported in two studies on linkage mapping of straighthead. This finding adds to previous work and is useful for further genetic study of straighthead.

Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 884-898 ◽  
Author(s):  
Jianjun Zhao ◽  
Anna Artemyeva ◽  
Dunia Pino Del Carpio ◽  
Ram Kumar Basnet ◽  
Ningwen Zhang ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Brassica Rapa ◽  
Core Collection ◽  
Field Experiments ◽  
Research Centre ◽  
Candidate Gene Approach ◽  
Core Collections ◽  
Genome Wide ◽  
Using Data

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

scholarly journals Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection

Genomics ◽  
2019 ◽  
Vol 111 (6) ◽  
pp. 1794-1801 ◽  
Author(s):  
Nathanael Fickett ◽  
Andres Gutierrez ◽  
Mohit Verma ◽  
Michael Pontif ◽  
Anna Hale ◽  
...  
Keyword(s):  
Association Mapping ◽  
Yield Components ◽  
Core Collection ◽  
Genome Wide Association ◽  
Cane Yield ◽  
Genome Wide

scholarly journals Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach

Heredity ◽  
2020 ◽  
Author(s):  
Panthita Ruang-areerate ◽  
Anthony J. Travis ◽  
Shannon R. M. Pinson ◽  
Lee Tarpley ◽  
Georgia C. Eizenga ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Mapping ◽  
Oryza Sativa L ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

2020 ◽  
Author(s):  
tengyue wang ◽  
Lijuan Wei ◽  
Jia wang ◽  
Ling Xie ◽  
Yangyang Li ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Association Mapping ◽  
Candidate Genes ◽  
Linkage Mapping ◽  
Growth Period ◽  
Phenotypic Traits ◽  
Multiple Traits ◽  
Brassica Napus L ◽  
Genome Wide ◽  
Ril Population

Abstract Background: Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus.Results: To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), days from initial flowering to final flowering (FP), days from final flowering to maturity (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, twelve candidate genes associated with growth period traits were identified in B. napus. Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. Conclusions: The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker assisted breeding for rapeseed adapted to different environments.

scholarly journals Association Mapping for Important Agronomic Traits in Core Collection of Rice (Oryza sativa L.) with SSR Markers

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e111508 ◽  
Author(s):  
Peng Zhang ◽  
Xiangdong Liu ◽  
Hanhua Tong ◽  
Yonggen Lu ◽  
Jinquan Li
Keyword(s):  
Oryza Sativa ◽  
Association Mapping ◽  
Ssr Markers ◽  
Core Collection ◽  
Agronomic Traits ◽  
Oryza Sativa L

scholarly journals Genome Wide Association Mapping of Grain Arsenic, Copper, Molybdenum and Zinc in Rice (Oryza sativa L.) Grown at Four International Field Sites

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e89685 ◽  
Author(s):  
Gareth J. Norton ◽  
Alex Douglas ◽  
Brett Lahner ◽  
Elena Yakubova ◽  
Mary Lou Guerinot ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Mapping ◽  
Oryza Sativa L ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Arsenic Copper
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