Genomic Selection for Drought Tolerance Using Genome-Wide SNPs in Maize

Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.

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Genome-wide association improves genomic selection for ammonia tolerance in the orange-spotted grouper (Epinephelus coioides)

Aquaculture ◽

10.1016/j.aquaculture.2020.736214 ◽

2021 ◽

Vol 533 ◽

pp. 736214

Author(s):

Xinxin Shan ◽

Tengfei Xu ◽

Zhiyuan Ma ◽

Xinhui Zhang ◽

Zhiqiang Ruan ◽

...

Keyword(s):

Genomic Selection ◽

Genome Wide Association ◽

Epinephelus Coioides ◽

Genome Wide ◽

Selection For ◽

Ammonia Tolerance

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Evaluation of Genomic Selection for Seven Economic Traits in Yellow Drum (Nibea albiflora)

Marine Biotechnology ◽

10.1007/s10126-019-09925-7 ◽

2019 ◽

Vol 21 (6) ◽

pp. 806-812 ◽

Cited By ~ 2

Author(s):

Guijia Liu ◽

Linsong Dong ◽

Linlin Gu ◽

Zhaofang Han ◽

Wenjing Zhang ◽

...

Keyword(s):

Genomic Selection ◽

Body Length ◽

Genome Wide Association Study ◽

Body Height ◽

Economic Traits ◽

Informative Snps ◽

Genome Wide ◽

Nibea Albiflora ◽

Selection For ◽

Swimming Bladder

AbstractYellow drum (Nibea albiflora) is an important maricultural fish in China, and genetic improvement is necessary for this species. This research evaluated the application of genomic selection methods to predict the genetic values of seven economic traits for yellow drum. Using genome-wide single-nucleotide polymorphisms (SNPs), we estimated the genetic parameters for seven traits, including body length (BL), swimming bladder index (SBI), swimming bladder weight (SBW), body thickness (BT), body height (BH), body length/body height ratio (LHR), and gonad weight index (GWI). The heritability estimates ranged from 0.309 to 0.843. We evaluated the prediction performance of various statistical methods, and no one method provided the highest predictive ability for all traits. We then evaluated and compared the use of genome-wide association study (GWAS)–informative SNPs and random SNPs for prediction and found that GWAS-informative SNPs obviously increased. It only needed 5 and 100 informative SNPs for LHR and BT to achieve almost the same predictive abilities as using genome-wide SNPs, and for BL, SBI, SBW, BH, and GWI, about 1000 to 3000 informative SNPs were needed to achieve whole-genome level predictive abilities. It can be concluded from the test results that breeders can use fewer SNPs to save the breeding costs of genomic selection for some traits.

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Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data

Frontiers in Plant Science ◽

10.3389/fpls.2018.00190 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 31

Author(s):

Yongle Li ◽

Pradeep Ruperao ◽

Jacqueline Batley ◽

David Edwards ◽

Tanveer Khan ◽

...

Keyword(s):

Drought Tolerance ◽

Association Mapping ◽

Genomic Selection ◽

Genome Wide Association ◽

Whole Genome ◽

Genome Resequencing ◽

Genome Wide ◽

Whole Genome Resequencing

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Yield gains and associated changes in an early yellow bi-parental maize population following genomic selection for Striga resistance and drought tolerance

BMC Plant Biology ◽

10.1186/s12870-019-1740-z ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

B. Badu-Apraku ◽

A. O. Talabi ◽

M. A. B. Fakorede ◽

Y. Fasanmade ◽

M. Gedil ◽

...

Keyword(s):

Drought Tolerance ◽

Genomic Selection ◽

Maize Population ◽

Striga Resistance ◽

Selection For

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Genome-wide association study of individual sugar content in fruit of Japanese pear (Pyrus spp.)

BMC Plant Biology ◽

10.1186/s12870-021-03130-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Sogo Nishio ◽

Takeshi Hayashi ◽

Kenta Shirasawa ◽

Toshihiro Saito ◽

Shingo Terakami ◽

...

Keyword(s):

Genomic Selection ◽

Candidate Genes ◽

Fruit Quality ◽

Sugar Content ◽

Genome Wide Association ◽

Sugar Accumulation ◽

Fruit Traits ◽

Chromosome 11 ◽

Genome Wide ◽

Selection For

Abstract Background Understanding mechanisms of sugar accumulation and composition is essential to determining fruit quality and maintaining a desirable balance of sugars in plant storage organs. The major sugars in mature Rosaceae fruits are sucrose, fructose, glucose, and sorbitol. Among these, sucrose and fructose have high sweetness, whereas glucose and sorbitol have low sweetness. Japanese pear has extensive variation in individual sugar contents in mature fruit. Increasing total sugar content and that of individual high-sweetness sugars is a major target of breeding programs. The objective of this study was to identify quantitative trait loci (QTLs) associated with fruit traits including individual sugar accumulation, to infer the candidate genes underlying the QTLs, and to assess the potential of genomic selection for breeding pear fruit traits. Results We evaluated 10 fruit traits and conducted genome-wide association studies (GWAS) for 106 cultivars and 17 breeding populations (1112 F1 individuals) using 3484 tag single-nucleotide polymorphisms (SNPs). By implementing a mixed linear model and a Bayesian multiple-QTL model in GWAS, 56 SNPs associated with fruit traits were identified. In particular, a SNP located close to acid invertase gene PPAIV3 on chromosome 7 and a newly identified SNP on chromosome 11 had quite large effects on accumulation of sucrose and glucose, respectively. We used ‘Golden Delicious’ doubled haploid 13 (GDDH13), an apple reference genome, to infer the candidate genes for the identified SNPs. In the region flanking the SNP on chromosome 11, there is a tandem repeat of early responsive to dehydration (ERD6)-like sugar transporter genes that might play a role in the phenotypes observed. Conclusions SNPs associated with individual sugar accumulation were newly identified at several loci, and candidate genes underlying QTLs were inferred using advanced apple genome information. The candidate genes for the QTLs are conserved across Pyrinae genomes, which will be useful for further fruit quality studies in Rosaceae. The accuracies of genomic selection for sucrose, fructose, and glucose with genomic best linear unbiased prediction (GBLUP) were relatively high (0.67–0.75), suggesting that it would be possible to select individuals having high-sweetness fruit with high sucrose and fructose contents and low glucose content.

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