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

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.

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

The Plant Genome ◽

10.1002/tpg2.20006 ◽

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

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Extreme‐phenotype genome‐wide association study ( XP ‐ GWAS ): a method for identifying trait‐associated variants by sequencing pools of individuals selected from a diversity panel

The Plant Journal ◽

10.1111/tpj.13029 ◽

2015 ◽

Vol 84 (3) ◽

pp. 587-596 ◽

Cited By ~ 44

Author(s):

Jinliang Yang ◽

Haiying Jiang ◽

Cheng‐Ting Yeh ◽

Jianming Yu ◽

Jeffrey A. Jeddeloh ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Extreme Phenotype ◽

Diversity Panel ◽

Genome Wide

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Quantile regression for genome-wide association study of flowering time-related traits in common bean

PLoS ONE ◽

10.1371/journal.pone.0190303 ◽

2018 ◽

Vol 13 (1) ◽

pp. e0190303 ◽

Cited By ~ 13

Author(s):

Moysés Nascimento ◽

Ana Carolina Campana Nascimento ◽

Fabyano Fonseca e Silva ◽

Leiri Daiane Barili ◽

Naine Martins do Vale ◽

...

Keyword(s):

Quantile Regression ◽

Association Study ◽

Common Bean ◽

Flowering Time ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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New genomic regions for resistance to anthracnose (Colletotrichum lindemuthianum) through GBS-based genome-wide association study in common bean (Phaseolus vulgaris)

World Journal of Advanced Research and Reviews ◽

10.30574/wjarr.2021.12.1.0493 ◽

2021 ◽

Vol 12 (1) ◽

pp. 020-040

Author(s):

Mariana Vaz Bisneta ◽

Maria Celeste Gonçalves-Vidigal ◽

Pedro Soares Vidigal Filho ◽

Júlio Cesar Ferreira Elias ◽

Giseli Valentini ◽

...

Keyword(s):

Association Study ◽

Common Bean ◽

Genome Wide Association Study ◽

Crop Improvement ◽

Gene Pyramiding ◽

Colletotrichum Lindemuthianum ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Genomic Regions

The most effective strategy to manage bean anthracnose (ANT), caused by Colletotrichum lindemuthianum, is the use of resistant cultivars. This study aimed to evaluate resistance reactions of common bean accessions to C. lindemuthianum races 2, 9 and 1545, and to perform genome-wide association study (GWAS). Hence, 89 accessions were phenotyped and genotyped through genotyping by sequencing (GBS). As a result, 48 accessions resistant to all evaluated races were identified. Moreover, single-nucleotide polymorphisms (SNP) significantly associated with resistance were identified in new regions of chromosomes Pv03, Pv05 and Pv06, and also at the beginning of Pv04 and end of Pv11, where other resistance genes have been previously found. In reference genome these regions contain model genes encoding resistance proteins as kinases, leucine-rich repeats, receptor-like protein, copper transport protein, pentatricopeptide repeats, calcium-dependent protein kinases, and ethylene-responsive transcription factors. The genomic regions associated to ANT resistance found in this study should be validated for further use in marker assisted selection and gene pyramiding. Together with new sources of ANT resistance our findings show promise for further crop improvement.

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