scholarly journals Selecting for Nut Characteristics in Macadamia Using a Genome-wide Association Study

HortScience ◽  
2019 ◽  
Vol 54 (4) ◽  
pp. 629-632 ◽  
Author(s):  
Katie O’Connor ◽  
Ben Hayes ◽  
Craig Hardner ◽  
Mobashwer Alam ◽  
Bruce Topp
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Selection Process ◽  
Kernel Weight ◽  
Snp Markers ◽  
Yield Component ◽  
Genome Wide Association ◽  
Shell Weight ◽  
Genome Wide ◽  
A Genome

Current macadamia breeding programs involve a lengthy and laborious two-stage selection process: evaluation of a large number of unreplicated seedling progeny, followed by replicated trials of clonally propagated elite seedlings. Yield component traits, such as nut-in-shell weight (NW), kernel weight (KW), and kernel recovery (KR) are commercially important, are more easily measured than yield, and have a higher heritability. A genome-wide association study (GWAS) combined with marker-assisted selection offers an opportunity to reduce the time of candidate evaluation. In this study, a total of 281 progeny from 32 families, and 18 of their 29 parents have been genotyped for 7126 single nucleotide polymorphism (SNP) markers. A GWAS was performed using ASReml with 4352 SNPs. We found five SNPs significantly associated with NW, nine with KW, and one with KR. Further, three of the top 10 markers for NW and KW were shared between the two traits. Future macadamia breeding could involve prescreening of individuals for desired traits using these significantly associated markers, with only predicted elite individuals continuing to the second stage of selection, thus potentially reducing the selection process by 7 years.

scholarly journals MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 25-33
Author(s):  
M. Ruiz ◽  
E.A. Rossi ◽  
N.C. Bonamico ◽  
M.G. Balzarini
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
Maize Germplasm ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

scholarly journals MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 25-33
Author(s):  
M. Ruiz ◽  
E.A. Ross ◽  
N.C. Bonamico ◽  
M.G. Balzarini
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
Maize Germplasm ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

scholarly journals A Genome-Wide Association Study for Resistance to the Insect Pest Leptocybe invasa in Eucalyptus grandis Reveals Genomic Regions and Positional Candidate Defense Genes

2020 ◽  
Vol 61 (7) ◽  
pp. 1285-1296
Author(s):  
Lorraine Mhoswa ◽  
Marja M O’Neill ◽  
Makobatjatji M Mphahlele ◽  
Caryn N Oates ◽  
Kitt G Payn ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Eucalyptus Grandis ◽  
Nucleotide Binding ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Leptocybe Invasa ◽  
Genomic Regions

Abstract The galling insect, Leptocybe invasa, causes significant losses in plantations of various Eucalyptus species and hybrids, threatening its economic viability. We applied a genome-wide association study (GWAS) to identify single-nucleotide polymorphism (SNP) markers associated with resistance to L. invasa. A total of 563 insect-challenged Eucalyptus grandis trees, from 61 half-sib families, were genotyped using the EUChip60K SNP chip, and we identified 15,445 informative SNP markers in the test population. Multi-locus mixed-model (MLMM) analysis identified 35 SNP markers putatively associated with resistance to L. invasa based on four discreet classes of insect damage scores: (0) not infested, (1) infested showing evidence of oviposition but no gall development, (2) infested with galls on leaves, midribs or petioles and (3) stunting and lethal gall formation. MLMM analysis identified three associated genomic regions on chromosomes 3, 7 and 8 jointly explaining 17.6% of the total phenotypic variation. SNP analysis of a validation population of 494 E. grandis trees confirmed seven SNP markers that were also detected in the initial association analysis. Based on transcriptome profiles of resistant and susceptible genotypes from an independent experiment, we identified several putative candidate genes in associated genomic loci including Nucleotide-binding ARC- domain (NB-ARC) and toll-interleukin-1-receptor-Nucleotide binding signal- Leucine rich repeat (TIR-NBS-LRR) genes. Our results suggest that Leptocybe resistance in E. grandis may be influenced by a few large-effect loci in combination with minor effect loci segregating in our test and validation populations.

scholarly journals The Minnesota Center for Twin and Family Research Genome-Wide Association Study

2012 ◽  
Vol 15 (6) ◽  
pp. 767-774 ◽  
Author(s):  
Michael B. Miller ◽  
Saonli Basu ◽  
Julie Cunningham ◽  
Eleazar Eskin ◽  
Steven M. Malone ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Generalized Least Squares ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Family Research ◽  
Genome Wide ◽  
A Genome ◽  
Array Quality ◽  
The Rich

As part of the Genes, Environment and Development Initiative, the Minnesota Center for Twin and Family Research (MCTFR) undertook a genome-wide association study, which we describe here. A total of 8,405 research participants, clustered in four-member families, have been successfully genotyped on 527,829 single nucleotide polymorphism (SNP) markers using Illumina's Human660W-Quad array. Quality control screening of samples and markers as well as SNP imputation procedures are described. We also describe methods for ancestry control and how the familial clustering of the MCTFR sample can be accounted for in the analysis using a Rapid Feasible Generalized Least Squares algorithm. The rich longitudinal MCTFR assessments provide numerous opportunities for collaboration.

Identification of a single genomic region associated with seasonal river return timing in adult Scottish Atlantic salmon (Salmo salar), using a genome-wide association study

2018 ◽  
Vol 75 (9) ◽  
pp. 1427-1435 ◽  
Author(s):  
Eef Cauwelier ◽  
John Gilbey ◽  
James Sampayo ◽  
Lee Stradmeyer ◽  
Stuart J. Middlemas
Keyword(s):  
Atlantic Salmon ◽  
Association Study ◽  
Salmo Salar ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Atlantic Salmon Salmo Salar ◽  
Genome Wide ◽  
A Genome ◽  
Run Timing

Examination of the genetic basis of the timing of the return migration of Atlantic salmon (Salmo salar) to fresh water from the sea, a trait of economic and conservation interest, was carried out using a genome-wide association study. We examined genotype data of 52 731 single nucleotide polymorphic (SNP) markers from 73 early and 49 late running two-sea-winter salmon from five rivers in eastern Scotland. A single region of the Atlantic salmon chromosome Ssa09 was identified, containing nine SNP markers significantly associated with run timing, a region previously linked to variation in sea age at maturity. Validation of the markers in a group of 233 one- and two-sea-winter fish, including adults from a novel river, again showed significant associations between the trait and the Ssa09 region, explaining ∼24% of the trait variance. The SNP loci identified provide the ability to examine trait variation in populations of Atlantic salmon and so help facilitate conservation management of the differing run timing phenotypes.

scholarly journals Genome wide association study reveals novel candidate genes associated with productivity and disease resistance to Moniliophthora spp. in cacao (Theobroma cacao L.)

2019 ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Jhon A. Berdugo-Cely ◽  
Roberto A. Coronado-Silva ◽  
Eliana Baez ◽  
Yeirme Jaimes ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Theobroma Cacao ◽  
Genome Wide Association Study ◽  
Economic Benefits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Moniliophthora Perniciosa ◽  
Genome Wide ◽  
A Genome

ABSTRACTCacao (Theobroma cacao L.), the source of chocolate, is one the most important commodity products for farmers to improve their economic benefits. However, diseases such as frosty pod rot (FPRD) caused by Moniliophthora roreri and witches’ broom (WBD) caused by Moniliophthora perniciosa, limits the increase in yields. Molecular tools can help to develop more rapidly cacao varieties with disease resistance. In the present study, we sequenced by genotyping-by-sequencing (GBS), 229 cacao accessions to examine their genetic diversity and population structure. From those accessions, 102 have been evaluated for disease resistance and productivity to conduct a genome-wide association study (GWAS) based on 9,003 and 8,131 SNPs recovered by mapping against to the annotated cacao genomes (Criollo and Matina). Three promissory accessions for productivity and 10 accessions showing good tolerance to the evaluated diseases were found in the phenotypic evaluation. The work presented herein provides the first association mapping study in cacao using SNP markers based on GBS data. The GWAS identified two genes associated to productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated to important traits in cacao that can have significant implications for conservation and breeding strategies such as marker-assisted selection (MAS).

scholarly journals A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0171105 ◽  
Author(s):  
Rodrigo Iván Contreras-Soto ◽  
Freddy Mora ◽  
Marco Antônio Rott de Oliveira ◽  
Wilson Higashi ◽  
Carlos Alberto Scapim ◽  
...  
Keyword(s):  
Association Study ◽  
Haplotype Analysis ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide association study and genomic selection for yield and related traits in soybean

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255761
Author(s):  
Waltram Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Qijian Song ◽  
Jin Yuan ◽  
...  
Keyword(s):  
Association Study ◽  
Genomic Selection ◽  
Plant Height ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Soybean [Glycine max (L.) Merr.] is a crop of great interest worldwide. Exploring molecular approaches to increase yield genetic gain has been one of the main challenges for soybean breeders and geneticists. Agronomic traits such as maturity, plant height, and seed weight have been found to contribute to yield. In this study, a total of 250 soybean accessions were genotyped with 10,259 high-quality SNPs postulated from genotyping by sequencing (GBS) and evaluated for grain yield, maturity, plant height, and seed weight over three years. A genome-wide association study (GWAS) was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model. Genomic selection (GS) was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that 20, 31, 37, and 23 SNPs were significantly associated with maturity, plant height, seed weight, and yield, respectively; Many SNPs were mapped to previously described maturity and plant height loci (E2, E4, and Dt1) and a new plant height locus was mapped to chromosome 20. Candidate genes were found in the vicinity of the two SNPs with the highest significant levels associated with yield, maturity, plant height, seed weight, respectively. A 11.5-Mb region of chromosome 10 was associated with both yield and seed weight. Overall, the accuracy of GS was dependent on the trait, year, and population structure, and high accuracy indicates that these agronomic traits can be selected in molecular breeding through GS. The SNP markers identified in this study can be used to improve yield and agronomic traits through the marker-assisted selection and GS in breeding programs.

scholarly journals Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Minmin Li ◽  
Ying Liu ◽  
Yahan Tao ◽  
Chongjing Xu ◽  
Xin Li ◽  
...  
Keyword(s):  
Association Study ◽  
Flowering Time ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Growth Period ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Genome Wide ◽  
A Genome

Abstract Background As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, we performed a genome-wide association study (GWAS) using a panel of 278 soybean accessions and 34,710 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) higher than 0.04 detected by the specific-locus amplified fragment sequencing (SLAF-seq) with a 6.14-fold average sequencing depth. GWAS was conducted by a compressed mixed linear model (CMLM) involving in both relative kinship and population structure. Results GWAS revealed that 37 significant SNP peaks associated with soybean flowering time or other growth periods related traits including full bloom, beginning pod, full pod, beginning seed, and full seed in two or more environments at -log10(P) > 3.75 or -log10(P) > 4.44 were distributed on 14 chromosomes, including chromosome 1, 2, 3, 5, 6, 9, 11, 12, 13, 14, 15, 17, 18, 19. Fourteen SNPs were novel loci and 23 SNPs were located within known QTLs or 75 kb near the known SNPs. Five candidate genes (Glyma.05G101800, Glyma.11G140100, Glyma.11G142900, Glyma.19G099700, Glyma.19G100900) in a 90 kb genomic region of each side of four significant SNPs (Gm5_27111367, Gm11_10629613, Gm11_10950924, Gm19_34768458) based on the average LD decay were homologs of Arabidopsis flowering time genes of AT5G48385.1, AT3G46510.1, AT5G59780.3, AT1G28050.1, and AT3G26790.1. These genes encoding FRI (FRIGIDA), PUB13 (plant U-box 13), MYB59, CONSTANS, and FUS3 proteins respectively might play important roles in controlling soybean growth periods. Conclusions This study identified putative SNP markers associated with soybean growth period traits, which could be used for the marker-assisted selection of soybean growth period traits. Furthermore, the possible candidate genes involved in the control of soybean flowering time were predicted.

PSXI-7 Genomic analysis of heterosis in a composite beef cattle breed

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 244-244
Author(s):  
El Hamidi Hay ◽  
Andrew Roberts
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Weaning Weight ◽  
Genome Wide ◽  
A Genome

Abstract Crossbreeding is widely used in the beef cattle industry to exploit benefits of heterosis. This study evaluated the effects of heterozygosity on growth traits in an Angus x Hereford cross population. Moreover, a genome wide association study was conducted to detect regions in the genome with significant dominance effects on growth traits contributing to heterosis. A total of 1,530 animals, comprised of pure Line 1 Hereford, Angus and Angus x Line 1 Hereford crosses, were evaluated. Phenotypes included birth weight, weaning weight and yearling weight. All animals were genotyped with GeneSeek GGP LD 50k. Effects of genomic heterozygosity on growth traits were estimated. These effects were -0.76 kg (P < 0.001), 4.67 kg (P < 0.0001), 42.39 kg (P < 0.02) on birth weight, weaning weight and yearling weight respectively. A genome wide association study revealed several SNP markers with significant heterotic effects associated with birth weight, weaning weight and yearling weight. These SNP markers were located on chromosomes 1, 2, 14, 19, 13 and 12. Genes in these regions were reported to be involved in growth and other important physiological mechanisms. Our study revealed several regions associated with dominance effects and contributing to heterosis. These results could be beneficial in optimizing crossbreeding.

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