Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

Background and aims: Vietnam harnesses a rich diversity of rice landraces adapted to a broad range of conditions, which constitute a largely untapped source of genetic diversity for the continuous improvement of rice cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica-5 group. Here, we leveraged on that strong differentiation, and the 672 rice genomes generated, to identify genes within genomic regions putatively selected during domestication and breeding of rice in Vietnam. Methodology: We identified significant distorted patterns in allele frequency (XP-CLR method) and population differentiation scores (FST), resulting from differential selective pressures between native subpopulations, and compared them with QTLs previously identified by GWAS in the same panel. We particularly focused on the outlying Indica-5 subpopulation because of its likely novelty and differential evolution. Results: We identified selection signatures in each of the Vietnamese subpopulations and carried out a comprehensive annotation of the 52 regions selected in Indica-5, which represented 8.1% of the rice genome. We annotated the 4,576 genes in these regions, verified the overlap with QTLs identified in the same diversity panel and the comparison with a FST analysis between subpopulations, to select sixty-five candidate genes as promising breeding targets, several of which harboured alleles with non-synonymous substitutions. Conclusions: Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.

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Identification of Selection Signatures in Commercial Asian Rice Subspecies Deciphered Selection Footprints for Four Overrepresented Biological Processes

10.21203/rs.3.rs-121958/v1 ◽

2020 ◽

Author(s):

Siavash Salek Ardestani ◽

Mahmoud Amiri Roudbar ◽

Mohammad Hossein Banabazi ◽

Seyedeh Fatemeh Mousavi ◽

Madhav Bhatta ◽

...

Keyword(s):

Selection Pressure ◽

Rice Genome ◽

Fixation Index ◽

Biological Processes ◽

Selection Signatures ◽

Genomic Changes ◽

Asian Rice ◽

Genome Level ◽

Window Approach ◽

Genomic Regions

Abstract BackgroundSelective breeding pressures have led to gradual genomic changes in Asian commercial rice, which have shaped selection footprints on its genome level. Tracing genomic selection footprints might be illuminative for better understanding of recent selection breeding objectives, and how breeding strategies have formed the Asian commercial rice genome. ResultsIn this study, the genotypic information (HDRA 700K) of four Asian commercial rice subspecies including Indica (n=498), Aus (n=187), Temperate japonica (n=241), and Tropical japonica (n=361) were downloaded from Rice Diversity Project database (http://www.ricediversity.org) to detect selection signatures by employing the Z-transformed of fixation index and Tajima’s D test, based on a sliding window approach. Although we could not identify overrepresented genomic regions underlying selection pressure among all aforementioned Asian commercial rice subspecies, interestingly, our findings revealed four overrepresented biological processes underlying selection pressure including proteolysis (GO:0006508), phosphorylation (GO:0016310), protein catabolic process (GO:0030163), and transmembrane transport (GO:0055085) that might be associated with immunity, senescing leaves, transporting, and absorption of ions. ConclusionsThese results can provide knowledge on how breeding efforts shaped the Asian commercial rice subspecies genome, and which genomic regions of these subspecies have been targeted in recent decades.

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Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Genes ◽

10.3390/genes10110938 ◽

2019 ◽

Vol 10 (11) ◽

pp. 938 ◽

Cited By ~ 4

Author(s):

Islam ◽

Li ◽

Liu ◽

Berihulay ◽

Abied ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Positive Selection ◽

Candidate Genes ◽

Runs Of Homozygosity ◽

Selection Signatures ◽

Effective Population ◽

Signature Of Selection ◽

Genomic Regions ◽

Insight Into

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

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Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

10.1101/2020.07.07.191981 ◽

2020 ◽

Author(s):

Janet Higgins ◽

Bruno Santos ◽

Tran Dang Khanh ◽

Khuat Huu Trung ◽

Tran Duy Duong ◽

...

Keyword(s):

Genetic Diversity ◽

Heading Date ◽

Cultivated Rice ◽

Region Of Origin ◽

Rice Varieties ◽

Rice Landraces ◽

Shared Ancestry ◽

Production Areas ◽

Genomic Regions ◽

New Generation

AbstractVietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. We identified genomic regions selected in both Indica and Japonica subtypes during the breeding of these subpopulations within Vietnam and discuss in detail fifty-two selected regions in I5, which constitute an untapped resource of cultivated rice diversity.Our results highlight traits and their associated genomic regions, which were identified by fine phenotyping and data integration. These are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

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Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

PLoS ONE ◽

10.1371/journal.pone.0242200 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242200

Author(s):

Natalia Anatolievna Zinovieva ◽

Arsen Vladimirovich Dotsev ◽

Alexander Alexandrovich Sermyagin ◽

Tatiana Evgenievna Deniskova ◽

Alexandra Sergeevna Abdelmanova ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Candidate Genes ◽

High Density ◽

Fixation Index ◽

Nucleotide Polymorphism ◽

Selection Signatures ◽

Single Nucleotide ◽

Cattle Breeds ◽

Native Cattle ◽

Genomic Regions

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

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Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

BMC Genomics ◽

10.1186/s12864-018-4690-1 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Elisabeth Le Bihan-Duval ◽

Christelle Hennequet-Antier ◽

Cécile Berri ◽

Stéphane A. Beauclercq ◽

Marie Christine Bourin ◽

...

Keyword(s):

Candidate Genes ◽

Chicken Meat ◽

Selection Signatures ◽

Genomic Regions ◽

Combined Detection

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Resequencing of 672 native rice accessions to explore genetic diversity and trait associations along Vietnam

10.21203/rs.3.rs-70697/v1 ◽

2020 ◽

Author(s):

Janet Higgins ◽

Bruno Santos ◽

Tran Dang Khanh ◽

Khuat Huu Trung ◽

Tran Duy Duong ◽

...

Keyword(s):

Genetic Diversity ◽

Heading Date ◽

Cultivated Rice ◽

Rice Varieties ◽

Rice Landraces ◽

Shared Ancestry ◽

Production Areas ◽

Genomic Regions ◽

New Generation ◽

Trait Associations

Abstract BACKGROUND: Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. RESULTS: We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. CONCLUSIONS: Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

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Genomewide Mapping of Selection Signatures and Genes for Extreme Feather Pecking in Two Divergently Selected Laying Hen Lines

Animals ◽

10.3390/ani10020262 ◽

2020 ◽

Vol 10 (2) ◽

pp. 262 ◽

Cited By ~ 3

Author(s):

Hanna Iffland ◽

Robin Wellmann ◽

Markus Schmid ◽

Siegfried Preuß ◽

Jens Tetens ◽

...

Keyword(s):

Candidate Genes ◽

Posterior Probability ◽

Negative Binomial ◽

Laying Hen ◽

Chromosome 1 ◽

Selection Signatures ◽

Genomewide Association Study ◽

Feather Pecking ◽

Binomial Distributions ◽

Genomic Regions

Feather pecking (FP) is a longstanding serious problem in commercial flocks of laying hens. It is a highly polygenic trait and the genetic background is still not completely understood. In order to find genomic regions influencing FP, selection signatures between laying hen lines divergently selected for high and low feather pecking were mapped using the intra-population iHS and the inter-population FST approach. In addition, the existence of an extreme subgroup of FP hens (EFP) across both selected lines has been demonstrated by fitting a mixture of negative binomial distributions to the data and calculating the posterior probability of belonging to the extreme subgroup (pEFP) for each hen. A genomewide association study (GWAS) was performed for the traits pEFP and FP delivered (FPD) with a subsequent post GWAS analysis. Mapping of selection signatures revealed no clear regions under selection. GWAS revealed a region on Chromosome 1, where the existence of a QTL influencing FP is likely. The candidate genes found in this region are a part of the GABAergic system, which has already been linked to FP in previous studies. Despite the polygenic nature of FP, selection on these candidate genes may reduce FP.

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Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types

Animals ◽

10.3390/ani10050773 ◽

2020 ◽

Vol 10 (5) ◽

pp. 773 ◽

Cited By ~ 1

Author(s):

Fuping Zhao ◽

Tianyu Deng ◽

Liangyu Shi ◽

Wenwen Wang ◽

Qin Zhang ◽

...

Keyword(s):

Candidate Genes ◽

Coat Color ◽

Reproductive Traits ◽

Bioinformatic Analysis ◽

Selection Signatures ◽

Selection Signature ◽

Positional Candidate ◽

Indigenous Sheep ◽

Tibetan Sheep ◽

Genomic Regions

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.

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Shared Ancestry and Signatures of Recent Selection in Gotland Sheep

Genes ◽

10.3390/genes12030433 ◽

2021 ◽

Vol 12 (3) ◽

pp. 433

Author(s):

Seyed Mohammad Ghoreishifar ◽

Christina Marie Rochus ◽

Sima Moghaddaszadeh-Ahrabi ◽

Pourya Davoudi ◽

Siavash Salek Ardestani ◽

...

Keyword(s):

Candidate Genes ◽

Growth Traits ◽

Significant Snps ◽

P Value ◽

Economic Traits ◽

Selection Signatures ◽

Shared Ancestry ◽

The Baltic ◽

Genomic Regions ◽

Recent Selection

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation FST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the FST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep.

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Multiple selection signatures in farmed Atlantic salmon adapted to different environments across Hemispheres

10.1101/525550 ◽

2019 ◽

Author(s):

M.E. López ◽

T. Linderoth ◽

A. Norris ◽

J.P. Lhorente ◽

R. Neira ◽

...

Keyword(s):

Atlantic Salmon ◽

Candidate Genes ◽

Complex Traits ◽

Score Test ◽

Selection Signatures ◽

Biological Mechanisms ◽

Extended Haplotype ◽

Selection Strategies ◽

Farmed Atlantic Salmon ◽

Genomic Regions

1.ABSTRACTDomestication of Atlantic salmon started approximately forty years ago, using both artificial and natural selection strategies. Such selection methods are likely to have imposed distinctive selection signatures on the salmon genome. Therefore, identifying differences in selection signatures may give insights into the mechanism of selection and candidate genes of biological and productive interest. Here, we used two complementary haplotype-based statistics, the within-population integrated Haplotype Score test (|iHS|) and the cross-population Extended Haplotype Homozygosity test (XP-EHH) to compare selection signatures in four populations of Atlantic salmon with a common genetic origin. Using |iHS| we found 24, 14, 16 and 26 genomic regions under selection in Pop-A, Pop-B, Pop-C, and Pop-D, respectively. While using the XP-EHH test we identified 27, 25 and 15 potential selection regions in Pop-A/Pop-B, Pop-A/Pop-C and Pop-A/Pop-D, respectively. These genomic regions harbor important genes such igf1r and sh3rf1 which have been associated with growth related traits in other species. Our results contribute to the detection of candidate genes of interest and help to understand the evolutionary and biological mechanisms for controlling complex traits under selection in Atlantic salmon.

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