Genome-environment associations in sorghum landraces predict adaptive traits.
Sci Adv. 2015 Jul;1(6):e1400218
Authors: Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Morris GP
Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.
PMID: 26601206 [PubMed - as supplied by publisher]
Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high density, high resolution consensus genetic map.
Plant J. 2015 Nov 21;
Authors: Tayeh N, Aluome C, Falque M, Jacquin F, Klein A, Chauveau A, Bérard A, Houtin H, Rond C, Kreplak J, Boucherot K, Martin C, Baranger A, Pilet-Nayel ML, Warkentin TD, Brunel D, Marget P, Le Paslier MC, Aubert G, Burstin J
SNP arrays represent important genotyping tools for innovative strategies in both basic research and applied breeding. Pea is an important food, feed, and sustainable crop with a large (ca. 4.45 Gb) and not yet available genome sequence. In the present study, 12 pea recombinant inbred line populations were genotyped using the newly-developed GenoPea 13.2K SNP Array. Individual and consensus genetic maps were built and explored providing insights into the pea genome structure and organization. Largely collinear 3,918 to 8,503-SNP genetic maps were obtained from all mapping populations and only two of these exhibited putative chromosomal rearrangement signatures. Similar distortion patterns in different populations were noted. Twelve thousand eight hundred two transcript-derived SNP markers placed on a 15,079-marker high density, high resolution consensus map allowed the identification of ohnolog-rich regions within the pea genome and the localization of local duplicates. Dense syntenic networks with sequenced legume genomes were further uncovered and established paving the way for the identification of the molecular bases of important agronomic traits segregating in the mapping populations. The information gained on the genome structure and organization from this research will undoubtedly contribute to the understanding of the genome evolution and to its assembly. The GenoPea 13.2K SNP Array and individual and consensus genetic maps are valuable genomic tools for the pea community to strengthen pea as a model for genetics and physiology and enhance breeding. This article is protected by copyright. All rights reserved.
PMID: 26590015 [PubMed - as supplied by publisher]
A Carbohydrate Sulfotransferase-6 (CHST6) gene mutation is associated with Macular Corneal Dystrophy in Labrador Retrievers.
Vet Ophthalmol. 2015 Nov 20;
Authors: Tetas Pont R, Downs L, Pettitt L, Busse C, Mellersh CS
PURPOSE: To locate and identify variants associated with macular corneal dystrophy (MCD) in Labrador Retriever (LR) dogs, in the candidate gene carbohydrate sulfotransferase-6 (CHST6).
METHODS: The single coding exon of canine CHST6 was sequenced in one affected LR with MCD and one control LR clinically clear of ocular disease. A further 71 control LR with unknown clinical status were sequenced for the putative causal variant in CHST6. A TaqMan SNP genotyping assay was developed and used to screen an additional 84 dogs (five affected LR and 79 clinically clear LR). Finally, the variant was screened in a third cohort of 89 unrelated LR with unknown clinical status to estimate its allele frequency in the population of LR in the United Kingdom.
RESULTS: A single nucleotide polymorphism (SNP) was identified within the coding exon of CHST6, resulting in a missense mutation (c.814C>A, p.R272S). All six LR affected with MCD were homozygous for the mutant allele, while 140/151 control LR were homozygous for the wild-type allele and 11/151 were heterozygous for the mutation, indicating an association with MCD (P < 10(-5) ). The mutant allele was present in the unrelated LR cohort at a frequency of 0.017, suggesting carrier and affection rates of 3.3% and 0.028%, respectively.
CONCLUSIONS: A missense mutation in the CHST6 gene is strongly associated with autosomal recessive MCD in the LR.
PMID: 26585178 [PubMed - as supplied by publisher]
Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array.
BMC Genomics. 2015;16(1):969
Authors: Tsai HY, Hamilton A, Tinch AE, Guy DR, Gharbi K, Stear MJ, Matika O, Bishop SC, Houston RD
BACKGROUND: The genetic architecture of complex traits in farmed animal populations is of interest from a scientific and practical perspective. The use of genetic markers to predict the genetic merit (breeding values) of individuals is commonplace in modern farm animal breeding schemes. Recently, high density SNP arrays have become available for Atlantic salmon, which facilitates genomic prediction and association studies using genome-wide markers and economically important traits. The aims of this study were (i) to use a high density SNP array to investigate the genetic architecture of weight and length in juvenile Atlantic salmon; (ii) to assess the utility of genomic prediction for these traits, including testing different marker densities; (iii) to identify potential candidate genes underpinning variation in early growth.
RESULTS: A pedigreed population of farmed Atlantic salmon (n = 622) were measured for weight and length traits at one year of age, and genotyped for 111,908 segregating SNP markers using a high density SNP array. The heritability of both traits was estimated using pedigree and genomic relationship matrices, and was comparable at around 0.5 and 0.6 respectively. The results of the GWA analysis pointed to a polygenic genetic architecture, with no SNPs surpassing the genome-wide significance threshold, and one SNP associated with length at the chromosome-wide level. SNPs surpassing an arbitrary threshold of significance (P < 0.005, ~ top 0.5 % of markers) were aligned to an Atlantic salmon reference transcriptome, identifying 109 SNPs in transcribed regions that were annotated by alignment to human, mouse and zebrafish protein databases. Prediction of breeding values was more accurate when applying genomic (GBLUP) than pedigree (PBLUP) relationship matrices (accuracy ~ 0.7 and 0.58 respectively) and 5,000 SNPs were sufficient for obtaining this accuracy increase over PBLUP in this specific population.
CONCLUSIONS: The high density SNP array can effectively capture the additive genetic variation in complex traits. However, the traits of weight and length both appear to be very polygenic with only one SNP surpassing the chromosome-wide threshold. Genomic prediction using the array is effective, leading to an improvement in accuracy compared to pedigree methods, and this improvement can be achieved with only a small subset of the markers in this population. The results have practical relevance for genomic selection in salmon and may also provide insight into variation in the identified genes underpinning body growth and development in salmonid species.
PMID: 26582102 [PubMed - as supplied by publisher]