scholarly journals Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.)

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Xiping Yang ◽  
Ziliang Luo ◽  
James Todd ◽  
Sushma Sood ◽  
Jianping Wang
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Yield Traits ◽  
Saccharum Spp ◽  
Diversity Panel ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Unravels LRK1 as a Dark Respiration Regulator in Rice (Oryza sativa L.)

2020 ◽  
Vol 21 (14) ◽  
pp. 4930
Author(s):  
Mingnan Qu ◽  
Jemaa Essemine ◽  
Ming Li ◽  
Shuoqi Chang ◽  
Tiangen Chang ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Study ◽  
Natural Variation ◽  
Genome Wide Association Study ◽  
Oryza Sativa L ◽  
Dark Respiration ◽  
Genome Wide Association ◽  
Strong Positive Correlation ◽  
Diversity Panel ◽  
Genome Wide

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (Rd) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with Rd. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that Rd shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. Rd also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of Rd collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high Rd. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% Rd of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of Rd in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

2011 ◽  
Vol 44 (1) ◽  
pp. 32-39 ◽  
Author(s):  
Xuehui Huang ◽  
Yan Zhao ◽  
Xinghua Wei ◽  
Canyang Li ◽  
Ahong Wang ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Flowering Time ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Yield Traits ◽  
Rice Germplasm ◽  
Genome Wide

scholarly journals A Genome-Wide Association Study Reveals Genes Associated with Fusarium Ear Rot Resistance in a Maize Core Diversity Panel

2013 ◽  
Vol 3 (11) ◽  
pp. 2095-2104 ◽  
Author(s):  
Charles T. Zila ◽  
L. Fernando Samayoa ◽  
Rogelio Santiago ◽  
Ana Butrón ◽  
James B. Holland
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Fusarium Ear Rot ◽  
Ear Rot ◽  
Diversity Panel ◽  
Genome Wide ◽  
A Genome

Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel

2021 ◽  
Author(s):  
Jessica Delfini ◽  
Vânia Moda-Cirino ◽  
José dos Santos Neto ◽  
Douglas Mariani Zeffa ◽  
Alison Fernando Nogueira ◽  
...  
Keyword(s):  
Association Study ◽  
Common Bean ◽  
Mineral Content ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Diversity Panel ◽  
Genome Wide

Identifying loci controlling fiber composition in polyploid sugarcane (Saccharum spp.) through genome-wide association study

2019 ◽  
Vol 130 ◽  
pp. 598-605 ◽  
Author(s):  
Xiping Yang ◽  
James Todd ◽  
Rebecca Arundale ◽  
Joseph B. Binder ◽  
Ziliang Luo ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Saccharum Spp ◽  
Fiber Composition ◽  
Genome Wide

scholarly journals Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

2018 ◽  
Author(s):  
Xiping Yang ◽  
Ziliang Luo ◽  
James Todd ◽  
Sushma Sood ◽  
Jianping Wang
Keyword(s):  
Association Study ◽  
Yield Components ◽  
Genome Wide Association Study ◽  
Crop Improvement ◽  
Dry Weight ◽  
Genome Wide Association ◽  
Sequence Variants ◽  
Diversity Panel ◽  
Fundamental Information ◽  
Genome Wide

AbstractSugarcane (Saccharum spp.) is an important economic crop, contributes up to 80% of sugar and approximately 60% bio-fuel globally. To meet the increased demand for sugar and bio-fuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield components. Therefore, dissection of causal DNA sequence variants is of great importance by providing genetic resources and fundamental information for crop improvement. In this study, we evaluated and analyzed nine yield components in a sugarcane diversity panel consisting of 308 accessions primarily selected from the “world collection of sugarcane and related grasses”. By genotyping the diversity panel using target enrichment sequencing, we identified a large number of sequence variants. Genome-wide association study between the markers and traits were conducted with dosages and gene actions taken into consideration. In total, 217 non-redundant markers and 225 candidate genes were identified to be significantly associated with the yield components, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs, and found that the occurrence of ROH in the genome were non-random and probably under selection. ROHs were associated with total weight and dry weight, and high ROHs resulted in decrease of the two traits. This study approved that genomic inbreeding has led to negative impacts on sugarcane yield.

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