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.

scholarly journals Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Leila Nayyeripasand ◽  
Ghasem Ali Garoosi ◽  
Asadollah Ahmadikhah
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Salinity Tolerance ◽  
Genome Wide Association Study ◽  
Dry Weight ◽  
Genome Wide Association ◽  
Vegetative Stage ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

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 identifies sequence variants on 6q21 associated with age at menarche

2009 ◽  
Vol 41 (6) ◽  
pp. 734-738 ◽  
Author(s):  
Patrick Sulem ◽  
Daniel F Gudbjartsson ◽  
Thorunn Rafnar ◽  
Hilma Holm ◽  
Elinborg J Olafsdottir ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Age At Menarche ◽  
Sequence Variants ◽  
Genome Wide

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

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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