Linkage Disequilibrium Decay Research Articles

SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China.

Single nucleotide polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism and, hence, are highly favorable markers for genetic map construction and genome-wide association studies. Based on the DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection, the genetic diversity and population structure of Salix gordejevii Y. L. Chang et Skv., a valuable sand-fixing shrub, was assessed in 199 accessions from 20 populations in Hunshandake Sandland of northern China. A total of 623.15M reads resulted in 30.49 × sequencing depth on average and a mean Q30 of 95.70%, and 2,287,715 SNPs in 178,509 polymorphic SLAF tags were obtained. By discarding minor allele frequency > 0.05 and integrity > 0.8, a total of 93,600 SNPs were retained for population genetic analyses, which revealed that 199 individuals could be divided into six groups based on cross-validation errors. However, this grouping pattern did not match the geographical distribution, indicating that there is no apparent geographic barrier in the blank areas where S. gordejevii was not distributed in Hunshandake Sandland. In addition, the physical distance of linkage disequilibrium decay in the analyzed S. gordejevii individuals was 18.5kb when r 2 = 0.1. The linkage disequilibrium decay distances for different chromosomes varied from 4.6kb (chromosome 16) to 37.8kb (chromosome 3). The obtained SNPs offer suitable marker resources for further genetic and genomic studies and will benefit S. gordejevii breeding programs.

Development of genome-wide single nucleotide polymorphism markers for variety identification of F1 hybrids in cucumber (Cucumis sativus L.)

Plant variety identification is essential for the official registration of new cultivars and for variety protection. It is therefore imperative to have rapid and highly reliable methods for plant variety identification. In this study, a core 96-SNP set optimized for use with Fluidigm EP1TM assay was developed to facilitate cultivar identification in cucumber. Genotyping-by-sequencing (GBS) of 88 F1 hybrids comprising nine cultivar groups (Korean Gasi, Korean Nakhap, Korean Baekdadagi, Japanese Gasi, Chinese Gasi, Chinese Baekdadagi, Southeast Asian slice, European slice, and pickle groups) was carried out, and a total of 10,996 high-quality SNPs were generated. Population structure, principle component analysis, and hierarchical clustering indicated that the nine cultivar groups were clearly divided into four subpopulations (subpopulation G for Gasi type, B for Baekdadagi type, N for Nakhap type, and E for slice and pickle types). Population differentiation measures based on pairwise FST values indicated that the closest relationship (0.124) was between subpopulations B and N and subpopulations E (0.140) and G, while subpopulations B and E were the most clearly distinct from each other (0.208). The metrics of genetic differentiation measured by AMOVA also indicated that significant genetic division exists among the subpopulations, while variation among cultivars within each subpopulation is extremely low, indicating high genetic exchange within the subpopulations. By applying filtering criteria to the SNPs, including FST and linkage disequilibrium decay values, 240 SNPs were filtered from the original 10,996 for use with a Fluidigm assay, from which a core 96-SNP set was obtained. This set demonstrated high reproducibility and discrimination power. Hierarchical clustering confirmed that the core 96-SNP set could distinguish all 88 cultivars and delineate them clearly according to their population structures. A Mantel test based on 10,996 SNPs and 37 traits revealed a high level of correlation (r = 0.57) between molecular and morphological distance. Our core 96-SNP set is not only suitable for generating signature profiles of released cucumber cultivars, but also represents a promising supplement to morphological trait-based distinctness, uniformity, and stability testing for cultivar identification.

Application of a novel 50K SNP genotyping array to assess the genetic diversity and linkage disequilibrium in a farmed Pacific white shrimp (Litopenaeus vannamei) population

The inclusion of genomic information became a reality in shrimp breeding and it is expected to accelerate the genetic gain over time. The decay of linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs) is an important measure to evaluate the feasibility of implementing genomic selection. The aim of this study was to evaluate the use of a novel 50 K SNP array tool to characterize the genomic diversity, LD and effective population size (Ne) in a farmed shrimp population. A total of 96 animals (40 sires and 56 dams) were genotyped using the novel Illumina AquaArray HD (50 K) vannamei®. Quality control (QC) of genomic data was performed and three different minor allele frequency (MAF) exclusion thresholds were applied: < 0.10 (QC1), < 0.05 (QC2) and < 0.01 (QC3). After QC, 34,425, 39,091 and 42,789 SNPs were retained for QC1, QC2 and QC3, respectively, validating the high informativeness of this SNP array to this particular shrimp breeding population. The population showed a considerable high overall heterozygosity in comparison to other aquaculture species meaning that genetic diversity is stable despite selection. The principal component analysis revealed three genetically distant groups with the first two principal components explaining 27.7 % of total variation. LD decayed rapidly in the first 30Kb of distance between markers from 0.20 to 0.07 and then decreased to 0.02 in the long-range distance. These results suggest a relatively recent incorporation of animals from different populations in the broodstock. Ne size reduced from 7,871 to 301 animals in 827 generations for QC1, 8,253 to 305 animals for QC2 and 8,957 to 315 animals for QC3, both in 899 generations. Contemporary Ne was close to 86 for all QCs. The level of LD estimated suggests that genomic selection and genome-wide association studies are feasible in shrimp by using this SNP array.

Genome-wide diversity analysis for signatures of selection of Bos indicus adaptability under extreme agro-climatic conditions of temperate and tropical ecosystems

Indigenous cattle breeds (Bos indicus) inhabited under diverse agroclimatic conditions may serve as a broad reservoir of genetic pool for identifying genes selected for local adaptation. The present study aimed at deciphering genomic diversity and identifying adaptation signatures of cattle breeds belonging to contrasting agro-climatic conditions: Siri and Ladakhi from cold hilly region; and Kankrej and Hallikar from hot arid and semi-arid regions, respectively. A total of 46 samples were genotyped using 777 K Illumina BovineHD BeadChip. The Principal Component Analysis brought together Hallikar and Kankrej, while Siri and Ladakhi formed a separate cluster. In contrast to the tropical cattle breeds, genetic variation was higher for temperate type. Linkage disequilibrium decay (r2 < 0.2) in hot semi-arid/arid adapted (71–103 kb) and temperate-adapted (218–222 kb) breeds revealed that BovineHD BeadChip can be used in predicting their genomic breeding values. Runs of homozygosity and FST based selection signatures were also identified in these cattle breeds. Novel hypoxia-related genes viz. egl-9 family hypoxia inducible factor, hypoxia inducible factor 1 subunit alpha inhibitor and heme oxygenase 1 were detected in temperate adapted breeds, while heat stress (heat shock protein family H (Hsp110) member 1 and BAG cochaperone 2 and immunity (TANK binding kinase 1) related genes were identified in selection sweeps of tropical breeds. Gene ontology analysis identified several enriched terms for the genes in both hot semi-arid/arid and temperate adapted cattle breeds in ROH islands. The relevant adaptation signals found in the present study will help to establish new breeding opportunities with recognition of core genes.

Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle.

Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree-based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH-based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009-2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P<0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.

Evaluating efficiency of customized medium density INDUSCHIP for genotyping of Indicine cattle breeds

To initiate genomic selection programme for indicine cattle breeds and their crosses in India, National Dairy Development Board designed a medium-density (52K) customized chip on Illumina platform named as “INDUSCHIP”. The present study was conducted to examine the efficiency of INDUSCHIP SNP panel for genotyping indicine cattle breeds. Total of 500 animals belonging to 14 different indicine breeds were genotyped with Illumina Bovine HD chip. A subset of SNPs was taken for evaluating the performance of selected SNPs in different indicine breeds. The average minor allele frequency (MAF) was found to vary between 0.20–0.29 for different indicine breeds. However, for important milk breeds like Sahiwal, Gir, Red Sindhi and Kankrej the average MAF was found to be 0.27 and above. Mean Linkage Disequilibrium (LD) at 50–60 kbp distance was found to be around 0.21. There was considerable LD decay with increasing distance between SNPs. Around 0.06% SNPs were found to be significantly deviating from Hardy-Weinberg equilibrium. From the Principal component analysis (PCA) it was found that the first three Principal Components i.e. PC1, PC2 and PC3) could separate different indicine breeds. The present study indicated that due to the presence of highly polymorphic SNPs for the breeds of indicine origin, INDUSCHIP panel was found to be effective and informative in genotyping indicine breeds.

TWAS results are complementary to and less affected by linkage disequilibrium than GWAS

A genome-wide association study (GWAS) is used to identify genetic markers associated with phenotypic variation. In contrast, a transcriptome-wide association study (TWAS) detects associations between gene expression levels and phenotypic variation. It has previously been shown that in the cross-pollinated species, maize (Zea mays), GWAS, and TWAS identify complementary sets of trait-associated genes, many of which exhibit characteristics of true positives. Here, we extend this conclusion to the self-pollinated species, Arabidopsis thaliana and soybean (Glycine max). Linkage disequilibrium (LD) can result in the identification, via GWAS, of false-positive associations. In all three analyzed plant species, most trait-associated genes identified via TWAS are well separated physically from other candidate genes. Hence, TWAS is less affected by LD than is GWAS, demonstrating that TWAS is particularly well suited for association studies in genomes with slow rates of LD decay, such as soybean. TWAS is reasonably robust to the plant organs/tissues used to determine expression levels. In summary, this study confirms that TWAS is a promising approach for accurate gene-level association mapping in plants that is complementary to GWAS, and established that TWAS can exhibit substantial advantages relative to GWAS in species with slow rates of LD decay.

High-throughput genotype-based population structure analysis of selected buffalo breeds.

India is considered as the home tract of some of the best buffalo breeds. However, the genetic structure of the Indian river buffalo is poorly understood. Hence, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds for selection and to design breeding strategies. In this study, we have analyzed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom Buffalo Genotyping Array. Diversity, as measured by expected heterozygosity, ranged from 0.364 in Surti to 0.384 in Murrah breed, and pair-wise FST values revealed the lowest genetic distance between Murrah and Nili-Ravi (0.0022), while the highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri, and Jaffarabadi in first two principal components and at K = 4, respectively, while remaining breeds were grouped together as a separate single cluster and admixed. Murrah and Mehsana showed early linkage disequilibrium (LD) decay, while Surti breed showed late decay. In LD blocks to quantitative trait locis (QTLs) concordance analysis, 4.65% of concordance was observed with 873 LD blocks overlapped with 2,330 QTLs. Overall, total 4,090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these single-nucleotide polymorphism (SNP) markers could differentiate phenotypically distinct breeds like Surti, Pandharpuri, and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds.

Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date

Key messageGenomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement.During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.

Association mapping reveals novel genomic regions controlling some root and stolon traits in tetraploid potato (Solanum tuberosum L.).

The online version contains supplementary material available at 10.1007/s13205-021-02727-6.

A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes

Conventional human leukocyte antigen (HLA) imputation methods drop their performance for infrequent alleles, which is one of the factors that reduce the reliability of trans-ethnic major histocompatibility complex (MHC) fine-mapping due to inter-ethnic heterogeneity in allele frequency spectra. We develop DEEP*HLA, a deep learning method for imputing HLA genotypes. Through validation using the Japanese and European HLA reference panels (n = 1,118 and 5,122), DEEP*HLA achieves the highest accuracies with significant superiority for low-frequency and rare alleles. DEEP*HLA is less dependent on distance-dependent linkage disequilibrium decay of the target alleles and might capture the complicated region-wide information. We apply DEEP*HLA to type 1 diabetes GWAS data from BioBank Japan (n = 62,387) and UK Biobank (n = 354,459), and successfully disentangle independently associated class I and II HLA variants with shared risk among diverse populations (the top signal at amino acid position 71 of HLA-DRβ1; P = 7.5 × 10−120). Our study illustrates the value of deep learning in genotype imputation and trans-ethnic MHC fine-mapping.

Genome-Wide Association of Stem Carbohydrate Accumulation and Remobilization during Grain Growth in Bread Wheat (Triticum aestivum L.) in Mediterranean Environments.

Water deficit represents an important challenge for wheat production in many regions of the world. Accumulation and remobilization of water-soluble carbohydrates (WSCs) in stems are part of the physiological responses regulated by plants to cope with water stress and, in turn, determine grain yield (GY). The genetic mechanisms underlying the variation in WSC are only partially understood. In this study, we aimed to identify Single Nucleotide Polymorphism (SNP) markers that account for variation in a suite of WSC and GY, evaluated in 225 cultivars and advanced lines of spring wheat. These genotypes were established in two sites in the Mediterranean region of Central Chile, under water-limited and full irrigation conditions, and assessed in two growing seasons, namely anthesis and maturity growth periods. A genome-wide association study (GWAS) was performed by using 3243 SNP markers. Genetic variance accounted for 5 to 52% of phenotypic variation of the assessed traits. A rapid linkage disequilibrium decay was observed across chromosomes (r2 ≤ 0.2 at 2.52 kbp). Marker-trait association tests identified 96 SNPs related to stem weight (SW), WSCs, and GY, among other traits, at the different sites, growing seasons, and growth periods. The percentage of SNPs that were part of the gene-coding regions was 34%. Most of these genes are involved in the defensive response to drought and biotic stress. A complimentary analysis detected significant effects of different haplotypes on WSC and SW, in anthesis and maturity. Our results evidence both genetic and environmental influence on WSC dynamics in spring wheat. At the same time, they provide a series of markers suitable for supporting assisted selection approaches and functional characterization of genes.

Genome-wide association studies of plant architecture-related traits and 100-seed weight in soybean landraces

BackgroundPlant architecture-related traits (e.g., plant height (PH), number of nodes on main stem (NN), branch number (BN) and stem diameter (DI)) and 100-seed weight (100-SW) are important agronomic traits and are closely related to soybean yield. However, the genetic basis and breeding potential of these important agronomic traits remain largely ambiguous in soybean (Glycine max (L.) Merr.).ResultsIn this study, we collected 133 soybean landraces from China, phenotyped them in two years at two locations for the above five traits and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). As a result, we found that a total of 59 SNPs were repeatedly detected in at least two environments. There were 12, 12, 4, 4 and 27 SNPs associated with PH, NN, BN, DI and 100-SW, respectively. Among these markers, seven SNPs (AX-90380587, AX-90406013, AX-90387160, AX-90317160, AX-90449770, AX-90460927 and AX-90520043) were large-effect markers for PH, NN, BN, DI and 100-SW, and 15 potential candidate genes were predicted to be in linkage disequilibrium (LD) decay distance or LD block. In addition, real-time quantitative PCR (qRT-PCR) analysis was performed on four 100-SW potential candidate genes, three of them showed significantly different expression levels between the extreme materials at the seed development stage. Therefore, Glyma.05 g127900, Glyma.05 g128000 and Glyma.05 g129000 were considered as candidate genes with 100-SW in soybean.ConclusionsThese findings shed light on the genetic basis of plant architecture-related traits and 100-SW in soybean, and candidate genes could be used for further positional cloning.

Population genetics and genome-wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce.

Genetic diversity is an important resource in crop breeding to improve cultivars with desirable traits. Selective breeding can lead to a reduction of genetic diversity. However, our understanding on this subject remains limited in lettuce (Lactuca sativa L.). Genotyping-by-sequencing (GBS) can provide a reduced version of the genome as a cost-effective method to identify genetic variants across the genome. We genotyped a diverse set of 441 lettuce accessions using the GBS method. Phylogenetic and population genetic analyses indicated substantial genetic divergence among four horticultural types of lettuce: butterhead, crisphead, leaf, and romaine. Genetic-diversity estimates between and within the four types indicated that the crisphead type was the most differentiated from other types, whereas its population was the most homogenous with the slowest linkage disequilibrium (LD) decay among the four types. These results suggested that crisphead lettuces had relatively less genetic variation across the genome as well as low gene flow from other types. We identified putative selective sweep regions that showed low genetic variation in the crisphead type. Genome-wide association study (GWAS) and quantitative trait loci (QTL) analyses provided evidence that these genomic regions were, in part, associated with delayed bolting, implicating the positive selection of delayed bolting in reducing variation. Our findings enhance the current understanding of genetic diversity and the impacts of selective breeding on patterning genetic variation in lettuce.

Genetic diversity and population structure of popcorn germplasm resources using genome-wide SNPs through genotyping-by-sequencing

Popcorn is a kind of snack food and has a breeding history of nearly 40 years in China, however, there are relatively few studies on its genetic diversity. Therefore, we present a genetic diversity and population structure analysis of 103 popcorn accessions, including 10 landraces from Latin America, 8 landraces from Southwest China and 76 and 9 popcorn breeding lines from China and the US, respectively, using polymorphic single-nucleotide polymorphisms (SNPs) developed by genotyping-by-sequencing. A total of 40,120 high-quality SNPs (19.21 SNPs per 1 Mb) were identified across the genome. Relative kinship analysis showed that the kinship coefficients for 0.3% of the pairs of lines were above 0.300, which agrees with the pedigree. The 103 accessions could be classified into three major groups based on model-based population structure, Neighbor-joining clustering, and principal component analysis based on the genetic background of the parents used for breeding. Group I consisted of landraces from both China and the Latin American countries, with some improved lines from landraces, while Group II and Group III consisted of lines primarily developed from popcorn commercial varieties, but with different levels of popping expansion ability. The average linkage disequilibrium decay distance in the entire panel under r2 < 0.1 was 0.28 Mb and varied among different groups, indicating a narrow genetic resource. The information provided in this study will be helpful for breeders to incorporate identified genetic variation into hybrid breeding programs.

Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

Brazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.

Genome-wide association analysis of Mexican bread wheat landraces for resistance to yellow and stem rust.

Deploying under-utilized landraces in wheat breeding has been advocated to accelerate genetic gains in current era of genomics assisted breeding. Mexican bread wheat landraces (Creole wheats) represent an important resource for the discovery of novel alleles including disease resistance. A core set of 1,098 Mexican landraces was subjected to multi-location testing for rust diseases in India, Mexico and Kenya. The landrace core set showed a continuous variation for yellow (YR) and stem rust (SR) disease severity. Principal component analysis differentiated Mexican landraces into three groups based on their respective collection sites. Linkage disequilibrium (LD) decay varied from 10 to 32 Mb across chromosomes with an averge of 23Mb across whole genome. Genome-wide association analysis revealed marker-trait associations for YR resistance in India and Mexico as well as for SR resistance in Kenya. In addition, significant additive-additive interaction effects were observed for both YR and SR resistance including genomic regions on chromosomes 1BL and 3BS, which co-locate with pleiotropic genes Yr29/Lr46/Sr58/Pm39/Ltn2 and Sr2/Yr30/Lr27, respectively. Study reports novel genomic associations for YR (chromosomes 1AL, 2BS, and 3BL) and SR (chromosomes 2AL, 4DS, and 5DS). The novel findings in Creole wheat landraces can be efficiently utilized for the wheat genetic improvement.

Genome-Wide Association Study of Tan Spot Resistance in a Hexaploid Wheat Collection From Kazakhstan.

Tan spot, caused by Pyrenophora tritici-repentis, is a serious foliar disease of wheat in Kazakhstan with reported yield losses as high as 50% during epidemic years. Here, we report the evaluation of a collection of 191 hexaploid spring and winter wheat lines for tan spot resistance and its underlying genetic architecture using genome-wide association study (GWAS). Our wheat collection comprised candidate varieties from Kazakhstan, Russia, and CIMMYT. It was genotyped using the DArTseq technology and phenotyped for resistance to tan spot at seedling and adult plant stages in Kazakhstan. DArTseq SNPs revealed high genetic diversity (average polymorphic information content = 0.33) in the panel and genome-wide linkage disequilibrium decay at 22 Mb (threshold r2 = 0.1). Principal component analysis revealed a clear separation of Eurasian germplasm from CIMMYT and IWWIP lines. GWAS identified 34 marker-trait associations (MTA) for resistance to tan spot and the amount of phenotypic variation explained by these MTA ranged from 4% to 13.7%. Our results suggest the existence of novel valuable resistant alleles on chromosomes 3BS, and 5DL and 6AL for resistance to Race 1 and Race 5, respectively, in addition to known genes tsn1 and tsc2. On chromosome 6AL, a genomic region spanning 3 Mb was identified conferring resistance to both Race 1 and Race 5. Epistatic interaction of associated loci was revealed on chromosomes 1B, 5B, 7B, 5A, and 6A contributing to additional variation of 3.2–11.7%. Twenty-five lines with the best allele combinations of SNPs associated with resistance to both races have been identified as candidates for future variety release and breeding. The results of the present study will be further validated in other independent genetic backgrounds to be able to use markers in breeding.

Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight

Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits.

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BackgroundNative cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle.ResultsThe population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6).ConclusionWe provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.