SNP Markers Research Articles

GENETIC CHARACTERIZATION IN FOUR INDONESIAN CATTLE BREEDS INFERRED FROM ILLUMINA PARENTAGE SNP MARKERS

Genetic characterization in native livestock is essential to conserve the genetics standard of livestock for pure-breeding programs. This research aimed to characterize four Indonesian cattle breeds using 156 sites of Parentage SNP Markers, includingARS-USMARC-Parent (119 sites) and ARS-USMARC (37 sites). Total of 113 mixed-sex animals were used for the evaluation, including 16 Bali (Bos javanicus), 16 Madura (Bos indicus), 33 Ongole grade (Bos indicus), and 48 Sumba Ongole (Bos indicus) cattle breeds. Results showed Bali, Madura, and Ongole lineage (Ongole grade and Sumba Ongole) cattle can be discriminated against with the Parentage SNP Markers. The pairwise genetic distance analysis revealed that Bali cattle had a closer genetic relationship with Madura cattle (0.043 - 0.151) than Ongole lineage cattle (0.073 - 0.325). However, the phylogenetic tree explained that the Ongole lineage cattle are grouped into two different clades. At the same time, Bali, Madura and Ongole lineage cattle are grouped into their original cluster. The study suggests that the Parentage SNP Markers can be used to characterize Bali, Madura, and Ongole lineage cattle accurately.

Quantitative Trait Loci Mapping for Adult-Plant Stripe Rust Resistance in Chinese Wheat Cultivar Weimai 8

Wheat stripe rust, triggered by Puccinia striiformis f. sp. tritici, is among the most widespread and damaging wheat (Triticum L.) diseases. The development of cultivars harboring adult plant resistance (APR) to stripe rust is a better approach to control the disease. The current study aimed to map APR to stripe rust via the QTL mapping of 165 F2–6 recombinant inbred lines (RILs), derivatives of Weimai 8/Zhengzhou 5389. The collection of phenotypic data for the stripe-rust resistance of both parents and all 165 RILs were conducted at Baoding, Hebei Province, during the 2016–2017 cropping seasons, and at Mianyang, Sichuan Province, during the 2017–2018 and 2018–2019 sowing seasons. The RIL populations and parents were also genotyped with 860 pairs of simple-sequence-repeat (SSR) primers to map APR QTLs to stripe-rust resistant. Moreover, a 55K SNP chip was used for small group bulk segregant analysis conducted to locate the genetic map location and concentration of the SNP markers on the wheat genome. Inclusive composite interval mapping (IciMapping 3.2) software identified four QTLs of stripe-rust resistance on chromosomes 1B, 2AS, 2BS, and 7DS, named QYr.wmy-1B, QYr.wmy-2AS, QYr.wmy-2BS, and QYr.wmy-7DS, which significantly explained 11.56–16.64%, 9.35–12.70%, 7.27–9.95%, and 11.49–15.07% of the phenotypic variation, respectively. All these QTLs were found from the resistant parent, Weimai 8. Meanwhile, the QTLs located on chromosomes 1B and 2AS were found close to Yr18 and Yr9, respectively. Furthermore, the results indicated that QYr.wmy-1B is possibly Yr9 and QYr.wmy-2AS is similar to Yr18 or might be a new QTL, whilst QYr.wmy-2BS and QYr.wmy-7DS were found to be different from previously reported stripe-rust-resistance QTLs and are possibly new QTLs. Overall, the QTLs and their closely associated molecular markers detected in this study could be a great source of input for marker-assisted selection to adult plant stripe-rust resistance in wheat-breeding programs.

Understanding the cocoa genetic resources in the Pacific to assist producers to supply the growing craft market

ABSTRACT The Pacific countries of Fiji, Samoa, Solomon Islands, and Vanuatu account for less than 2% of the world’s cacao dry bean production. To capitalise on the rapidly expanding origin craft cocoa market, understanding the genetic attributes of Theobroma cacao in the Pacific is essential. A six-year ACIAR-funded project collected 1647 dried leaf samples from research stations and smallholder farms to identify the population ancestry of T. cacao in the partner countries. Using SNP marker profiling, the study identified germplasm high in Amelonado, which represents the majority of material throughout the Pacific. However, the study also identified samples high in the remaining nine genetic groups, including Criollo, Nanay, IMC (Iquitos), Guiana, Parinari (Marañón), Nacional, Ucayali (Contamana), LCT EEN (Curaray), and Purus, which were distributed throughout the Pacific. The results, if utilised in local selection trials, could reposition growers in the Pacific countries, allowing them to supply the growing origin craft cocoa market, with genetically unique beans. Cocoa genetics was one aspect of a project incorporating production and postharvest research to refocus the commodity based cocoa industry to a supplier of high-quality beans of unique Pacific cocoa origin to the rapidly expanding craft ‘bean to bar’ cocoa industry.

Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding

Genetic diversity is fundamental for studying the complex architecture of the traits of agronomic importance, controlled by major and minor loci. Moreover, well-characterized germplasm collections are essential tools for dissecting and analyzing genetic and phenotypic diversity in crops. A panel of 360 entries, a subset of a larger collection maintained within the GenBank at CREA Bergamo, which includes the inbreds derived from traditional Italian maize open-pollinated (OP) varieties and advanced breeding ones (Elite Inbreds), was analyzed to identify SNP markers using the tGBS® genotyping-by-sequencing technology. A total of 797,368 SNPs were found during the initial analysis. Imputation and filtering processes were carried out based on the percentage of missing data, redundant markers, and rarest allele frequencies, resulting in a final dataset of 15,872 SNP markers for which a physical map position was identified. Using this dataset, the inbred panel was characterized for linkage disequilibrium (LD), genetic diversity, population structure, and genetic relationships. LD decay at a genome-wide level indicates that the collection is a suitable resource for association mapping. Population structure analyses, which were carried out with different clustering methods, showed stable grouping statistics for four groups, broadly corresponding to ‘Insubria’, ‘Microsperma’, and ‘Scagliolino’ genotypes, with a fourth group composed prevalently of elite accessions derived from Italian and US breeding programs. Based on these results, the CREA Italian maize collection, genetically characterized in this study, can be considered an important tool for the mapping and characterization of useful traits and associated loci/alleles, to be used in maize breeding programs.

Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut.

Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.

Using NGS Technology and Association Mapping to Identify Candidate Genes Associated with Fusarium Stalk Rot Resistance.

Stalk rot caused by Fusarium fungi is one of the most widespread and devastating diseases of maize, and the introduction of resistant genotypes is one of the most effective strategies for controlling the disease. Breeding genotypes with genetically determined resistance will also allow less use of crop protection products. The aim of the research was to identify molecular markers and associated candidate genes determining maize plant resistance to Fusarium stalk rot. The plant material for this study consisted of 122 maize hybrids. The experiment was conducted in two localities: Smolice and Kobierzyce. The Fusarium stalk rot values ranged from 1.65% (for genotype G01.10) to 31.18% (for genotype G03.07) in Kobierzyce and from 0.00% (for 58 genotypes) to 6.36% (G05.03) in Smolice. The analyzed genotypes were simultaneously subjected to next-generation sequencing using the Illumina platform. Illumina sequencing identified 60,436 SilicoDArT markers and 32,178 SNP markers (92,614 in total). For association mapping, 32,900 markers (26,234 SilicoDArT and 6666 SNP) meeting the criteria (MAF > 0.25 and the number of missing observations <10%) were used. The results of the observation of the degree of infection and sequencing were used for association mapping, which ultimately resulted in the selection of ten molecular markers important at both places. Among the identified markers, two SNP markers that are located inside candidate genes play an important role. Marker 4772836 is located inside the serine/threonine-protein kinase bsk3 gene, while marker 4765764 is located inside the histidine kinase 1 gene. Both genes can be associated with plant resistance to Fusarium stalk rot, and these genes can also be used in breeding programs to select resistant varieties.

Genome-wide association analysis to identify genomic regions and predict candidate genes for bunch traits in grapes (Vitis vinifera L.)

Grape quality traits like bunch and berry size are important as they influence consumer acceptance and marketability of the produce. Therefore, a deeper understanding of their genetic determinant is crucial for varietal improvement. In this study, association mapping was performed using SNP marker data and three season phenotyping data of 122 diverse grapevine genotypes. Genotyping by sequencing (GBS) identified 1,08,777 high quality SNPs distributed on all the chromosomes. A good correlation was observed across three seasons for berry size and bunch length. Genome-wide association analysis using six different models identified significantly associated SNPs for each of the traits. We identified 13 significant SNPs associated with bunch length, seven of them were located on linkage groups (LGs) 9 and 15. For berry diameter, 18 significantly associated markers located on LGs 4, 5, 17 and six other LGs were identified. Fourteen SNPs mainly on linkage groups 3 and 5 were identified for berry weight. Three closely linked markers on LG3 explaining about 20-25 % variation suggested presence of major QTL for berry weight on LG3. Candidate genes were mined in the genomic regions containing significant SNPs explaining large phenotypic variation. Twenty-one genes for bunch length, 28 genes for berry length, 22 genes for berry diameter and 25 genes for berry weight were predicted. Several predicted genes were found to have function related to cell enlargement, cell morphogenesis and other physiological processes required for cell growth and development.

Deciphering the genetic architecture of anther culturability in rice using segregation distortion approach

AbstractAnther culture is a promising technique used in rice (Oryza sativa L.) breeding, although the genetic mechanisms associated with anther culturability remain elusive. In the process of in vitro anther culture, favorable alleles for anther culture are preferentially transmitted to doubled haploid (DH) populations, resulting in biased segregation of DH populations. Therefore, the segregation distortion (SD) method is an ideal approach for mapping the genetic loci controlling anther culturability. Performing a SD analysis using a genetic map consisting of 666 single nucleotide polymorphism markers, we identified five potential loci (logarithm of odds [LOD] &gt; 3.5) that may be associated with anther culturability, including SDL2 and SDL3, which are overrepresented in japonica alleles, and SDL7, SDL9, and SDL11, which are overrepresented in indica alleles. In addition, nine pairs of epistatic interactions (EPIs) that contribute significantly (p &lt; 0.05) to SD in the DH population were identified. Among them, the interaction between SDL2 and SDL3 is particularly noteworthy. These findings suggest that anther culturability in rice is governed by complex genetic mechanisms involving multiple nuclear genes and EPIs. This study provides insights into the genetic control underlying anther culturability in rice and lays the foundation for future research aimed at identifying causal genes associated with anther culturability.

Genomic resources for a historical collection of cultivated two-row European spring barley genotypes

Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.

Multi-model genome-wide association studies for appearance quality in rice.

Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.

Genome-wide SNP markers provided insights into the reproductive strategy and genetic diversity of the green tide causative species Ulva prolifera in China

Genome-wide SNP markers provided insights into the reproductive strategy and genetic diversity of the green tide causative species Ulva prolifera in China

Gender specific SNP markers in Coscinium fenestratum (Gaertn.) Colebr. for resource augmentation.

Unregulated extraction of highly traded medicinal plant species results in drastic decline of the natural resources and alters viable sex ratio of populations. Conservation and long-term survival of such species, require gender specific restoration programs to ensure reproductive success. However, it is often difficult to differentiate sex of individuals before reaching reproductive maturity. C. fenestratum is one of the medicinally important and overexploited dioecious woody liana, with a reproductive maturity of 15 years. Currently, no information is available to identify sex of C. fenestratum in seedling stage while augmenting the resources. Thus, the current study envisages to utilize transcriptomics approach for gender differentiation which is imperative for undertaking viable resource augmentation programmes. Gender specific SNPs with probable role in sexual reproduction/sex determination was located using comparative transcriptomics approach (sampling male and female individuals), alongside gene ontology and annotation. Nine sets of primers were synthesized from 7 transcripts (involved in sexual reproduction/other biological process) containing multiple SNP variants. Out of the nine primer pairs, only one SNP locus with no available information of its role in reproduction, showed consistent and accurate results (males-heterozygous and females-homozygous), in the analyzed 40 matured individuals of known sexes. Thus validated the efficiency of this SNP marker in differentiating male and female individuals. The study could identify SNPs linked to the loci with apparent role in gender differentiation. This SNP marker can be used for early sexing of seedlings for in-situ conservation and resource augmentation of C. fenestratum in Kerala, India.

Genetic diversity analysis of different geographic populations of black carp (Mylopharyngodon piceus) based on whole genome SNP markers

Black carp, Mylopharyngodon piceus, is one of the major farmed fish in China, generating a considerable amount of economic value annually. To investigate the genetic variation of black carp germplasm resources in China, this study was the first to use the whole genome SNPs of black carp for analysis. A total of 139 samples of nine black carp populations in the Yangtze River and Pearl River Systems of China were collected, and 53,322 high-quality SNP loci were obtained after GBS sequencing and filtering. Genetic diversity parameters were calculated for nine populations of black carp based on these genetic data. All 7 populations from the Yangtze River system and 2 populations from the Pearl River system showed high level of genetic diversity. For each population, the nucleotide diversity (π) varied from 0.283 to 0.308, the observed heterozygosity (Ho) from 0.271 to 0.317, the expected heterozygosity (He) from 0.273 to 0.292，the number of effective alleles (Ne) from 1.440 to 1.475, and the polymorphism information content (PIC) from 0.224 to 0.239. The fixation index (Fst) between populations ranged from 0.036 to 0.133, remaining at low and medium differentiation. Phylogenetic tree analysis, principal component analysis (PCA) and population genetic structure analysis revealed that the nine populations could be divided into three ancestral populations. The seven populations of the Yangtze River system comprised two primary ancestral groups, with a small amount of gene flow between populations. The internal genetic structure of populations within the Pearl River system was homogeneous, with one common ancestral source as the dominant component. In conclusion, the data and results generated from this study will provide a useful addition to the genetic resources of black carp and will provide reference information for further germplasm conservation and genetic improvement of black carp.

Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers.

The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., 'Saccharum spp', 'unknown', and 'hybrid'). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor-joining clustering analysis. Analysis of Molecular Variance revealed that within-species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement.

Association of hard fescue (Festuca brevipila) stress tolerances with genome mapped markers

AbstractHard fescue is an allo‐hexaploid, caespitose, cool‐season grass that is part of the fine‐leaved ovina complex of the Lolium–Festuca clade in Poaceae. It is predominantly used as a low‐maintenance turfgrass and soil stabilization grass in situations with reduced inputs of nitrogen and water. While often recommended for use under tree canopies, prolonged foliar shade can thin turf stands and reduce their functionality; furthermore, gray snow mold caused by Typhula incarnata can further affect hard fescue turfgrass functionality. In this study, we gathered a diverse population of hard fescue collections and varieties, which fit into four genetic structures. Because no genomic reference sequences exist for this species, a contig‐level pseudohaploid genomic reference was assembled from a plant of the hard fescue variety Beacon. With 98% benchmarking universal single‐copy orthologs (BUSCO) coverage from 241 contigs, this reference assembly was used to conduct genome‐wide association analysis. Thirty‐eight single‐nucleotide polymorphism (SNP) markers were associated with foliar shade response phenotypes, including SNPs near molybdate transporter and cytochrome P450 genes. Three SNP markers were associated with gray snow mold responses, with one located near a Protein Kinase G11 gene and corresponding to a 20% improvement in gray snow mold resistance.

Genome-wide association study of agronomic traits related to nitrogen use efficiency in Henan wheat

BackgroundNitrogen use efficiency (NUE) is closely related to crop yield and nitrogen fertilizer application rate. Although NUE is susceptible to environments, quantitative trait nucleotides (QTNs) for NUE in wheat germplasm populations have been rarely reported in genome-wide associated study.ResultsIn this study, 244 wheat accessions were phenotyped by three NUE-related traits in three environments and genotyped by 203,224 SNPs. All the phenotypes for each trait were used to associate with all the genotypes of these SNP markers for identifying QTNs and QTN-by-environment interactions via 3VmrMLM. Among 279 QTNs and one QTN-by-environment interaction for low nitrogen tolerance, 33 were stably identified, especially, one large QTN (r2 > 10%), qPHR3A.2, was newly identified for plant height ratio in one environment and multi-environment joint analysis. Among 52 genes around qPHR3A.2, four genes (TraesCS3A01G101900, TraesCS3A01G102200, TraesCS3A01G104100, and TraesCS3A01G105400) were found to be differentially expressed in low-nitrogen-tolerant wheat genotypes, while TaCLH2 (TraesCS3A01G101900) was putatively involved in porphyrin metabolism in KEGG enrichment analyses.ConclusionsThis study identified valuable candidate gene for low-N-tolerant wheat breeding and provides new insights into the genetic basis of low N tolerance in wheat.

Establishment and application of a SNP molecular identification system in Grifola frondosa.

Germplasm resources of edible mushrooms are essential for the breeding of varieties with improved traits. Analysis of the genetic diversity of Grifola frondosa germplasm resources and clarification of the genetic relationships among strains can provide valuable information for the selection of breeding parents. A total of 829,488 high-quality SNP loci were screened from 2,125,382 SNPs obtained by sequencing 60 G. frondose. Phylogenetic analysis, PCA, and population structure analysis based on the high-quality SNPs showed that the 60 strains could be divided into five subgroups, and the clustering results were consistent with the geographical distributions of these strains. Based on high-quality SNP loci, a core collection containing 18 representative germplasm resources was constructed, and 1,473 Kompetitive Allele-Specific PCR markers were obtained. A total of 722 SNP markers in the exonic regions were screened using KASP-genotyping experiments, and 50 candidate SNP markers and 12 core SNP markers were obtained. Genetic fingerprints of G. frondosa germplasm resources were constructed based on the selected SNP markers; these fingerprints provide an accurate, rapid, convenient, and efficient method for the identification of G. frondosa germplasm resources. The results of this study have important implications for the preservation and utilization of G. frondosa germplasm resources and the identification of varieties.

Development and parentage analysis of SNP markers for Chestnut-vented Nuthatch (Sitta nagaensis) based on ddRAD-seq data

Extra-pair paternity (EPP) is commonly found in socially monogamous birds, especially in small passerine birds, and there are interspecific and intraspecific variations in the extent of EPP. The Chestnut-vented Nuthatch (Sitta nagaensis) is a socially monogamous passerine bird, and verifying whether this species has EPP relies on parentage testing—S. nagaensis is not known to have EPP. In this study, we developed SNP markers of this species that are informative for parentage analysis from double digest restriction site-associated DNA sequencing (ddRAD-seq) data. A panel consisting of 50 SNP markers, with a mean heterozygosity of 0.343, was used to resolve 95% of nestlings to fathers. The combined exclusion probabilities for the first parent and second parent were 0.991 and 0.9999, respectively. This panel of SNP markers is a powerful tool for parentage assignments in S. nagaensis. In addition, we found that three offspring (7.9%) from three nests (23.1%) were the result of extra-pair fertilization out of 38 offspring in 13 nests. Our study provided information on parentage analysis that has not been reported before in S. nagaensis. It also supplemented the understudied EPP behavior of birds in Asia, contributing to a general understanding of the EPP behaviors of birds.

Genomic Selection as an Approach to Select for Reduced Aflatoxin Contamination in Peanut Under Terminal Drought Stress

Pre-harvest aflatoxin contamination (PAC) occurs when the peanut is exposed to severe drought and heat stress prior to harvest. Development of genotypes that are either resistant or limiting to Aspergillus infection and/or that can curtail aflatoxin production is a key objective in peanut breeding. Using SNP markers and phenotype data on aflatoxin resistance collected in previous years, we utilized genomic selection (GS) to study PAC resistance in peanut. The technique was validated in the Florida-07 x GP-NC WS 16 recombinant inbred population by assessing high heritability traits. GS was then deployed to study PAC resistance in the Tifrunner x C76-16 and Florida-07 x C76-16 populations. The resultant models yielded prediction accuracy values of 0.24 and 0.23 which while low, were comparable to the heritability values of 0.31 and 0.1 for each population, respectively. Using genomic estimated breeding values (GEBVs), entries were selected for two drought shelter studies. Manual scoring and multispectral imaging were used to acquire end season drought stress data. Low correlation values (-0.15 for shelter A and 0.32 for shelter B) were observed between the GEBVs and actual end season aflatoxin content. Correlations between visual drought ratings and PAC were also low (0.23 and 0.16 for shelter A and B respectively). While strong inverse correlations were observed between GNDVI and visual drought ratings (-0.74 and -0.73 for shelters A and B respectively), GNDVI did not confer a clear advantage for selection of PAC resistance. Ideally, the use of genome-spanning markers in GS may enable selection for a difficult to phenotype trait like PAC resistance. Although this study did not show clear advantages of the method over conventional selection, it is an important step for implementation of GS and the use of GEBVs for trait selection in peanut.

Growth hormone gene polymorphism in domestic and wild goat breeds in Kurdistan region of Iraq using PCR-RFLP and SNP markers

Growth hormone gene polymorphism in domestic and wild goat breeds in Kurdistan region of Iraq using PCR-RFLP and SNP markers