scholarly journals Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii

2021 ◽  
Author(s):  
Kumar Gaurav ◽  
Sanu Arora ◽  
Paula Silva ◽  
Javier Sánchez-Martín ◽  
Richard Horsnell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Candidate Genes ◽  
Bread Wheat ◽  
Aegilops Tauschii ◽  
Pest Resistance ◽  
Wild Progenitor ◽  
Genomic Regions ◽  
Synthetic Hexaploids ◽  
Diploid Ancestor

AbstractAegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242 Ae. tauschii accessions and compared them to the wheat D-subgenome. We characterized a rare, geographically-restricted lineage of Ae. tauschii and discovered that it contributed to the wheat D-subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then used k-mer-based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of ‘synthetic’ hexaploids incorporating diverse Ae. tauschii genomes. This pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation in a hexaploid background amenable to breeding.

scholarly journals Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

2021 ◽  
Author(s):  
Kumar Gaurav ◽  
Sanu Arora ◽  
Paula Silva ◽  
Javier Sánchez-Martín ◽  
Richard Horsnell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Bread Wheat ◽  
Aegilops Tauschii ◽  
Genomic Analysis ◽  
Genomic Diversity ◽  
Wild Progenitor ◽  
Population Genomic ◽  
Wheat Improvement ◽  
Genomic Regions

AbstractAegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

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

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 938 ◽  
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.

scholarly journals Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

2019 ◽  
Author(s):  
Jaime Osorio ◽  
Gina Garzón ◽  
Paola Delgadillo ◽  
Silvio Bastidas ◽  
Leidy Moreno ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Oil Palm ◽  
Plant Architecture ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis , Elaeis oleifera , genotyping-by-sequencing, plant architecture, yield.

scholarly journals Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Pedro H. F. Freitas ◽  
Yachun Wang ◽  
Ping Yan ◽  
Hinayah R. Oliveira ◽  
Flavio S. Schenkel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Thermal Tolerance ◽  
Climatic Conditions ◽  
Biological Processes ◽  
Biological Mechanisms ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Selection For ◽  
Genomic Regions

Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (FST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.

scholarly journals Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sirous Eydivandi ◽  
Mahmoud Amiri Roudbar ◽  
Mohammad Osman Karimi ◽  
Goutam Sahana
Keyword(s):  
Genetic Diversity ◽  
Middle East ◽  
South Asia ◽  
Candidate Genes ◽  
Genotype Data ◽  
Extended Haplotype Homozygosity ◽  
Selective Sweeps ◽  
Extended Haplotype ◽  
Indigenous Sheep ◽  
Genomic Regions

AbstractThe performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.

scholarly journals Genome wide association study (GWAS) for morphological and yield-related traits in oil palm hybrids (Elaeis oleifera x Elaeis guineensis)

2019 ◽  
Author(s):  
Jaime Osorio ◽  
Gina Garzón ◽  
Paola Delgadillo ◽  
Silvio Bastidas ◽  
Leidy Moreno ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Oil Palm ◽  
Plant Architecture ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
Genomic Regions

Abstract Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. The work presented herein provides, to our knowledge, the first association mapping study in an interspecific OxG hybrid population of oil palm which presents tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrids for 10 agronomic traits. Twelve genomic regions were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on candidate genes that mapped on genomic regions involved in plant architecture and yield; however, these potential candidate genes need to be confirmed for future targeted functional analysis. The associated markers may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis, Elaeis oleifera, genotyping-by-sequencing, plant architecture, yield.

scholarly journals Genome-Wide Association Study of Morpho-Physiological Traits in Aegilops tauschii to Broaden Wheat Genetic Diversity

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 211
Author(s):  
Mazin Mahjoob Mohamed Mahjoob ◽  
Yasir Serag Alnor Gorafi ◽  
Nasrein Mohamed Kamal ◽  
Yuji Yamasaki ◽  
Izzat Sidahmed Ali Tahir ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bread Wheat ◽  
Association Studies ◽  
Aegilops Tauschii ◽  
Genome Wide Association ◽  
Physiological Traits ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Wide Range ◽  
Or Genes

Aegilops tauschii, the D-genome donor of bread wheat, is a storehouse of genetic diversity that can be used for wheat improvement. This species consists of two main lineages (TauL1 and TauL2) and one minor lineage (TauL3). Its morpho-physiological diversity is large, with adaptations to a wide ecological range. Identification of allelic diversity in Ae. tauschii is of utmost importance for efficient breeding and widening of the genetic base of wheat. This study aimed at identifying markers or genes associated with morpho-physiological traits in Ae. tauschii, and at understanding the difference in genetic diversity between the two main lineages. We performed genome-wide association studies of 11 morpho-physiological traits of 343 Ae. tauschii accessions representing the entire range of habitats using 34,829 DArTseq markers. We observed a wide range of morpho-physiological variation among all accessions. We identified 23 marker–trait associations (MTAs) in all accessions, 15 specific to TauL1 and eight specific to TauL2, suggesting independent evolution in each lineage. Some of the MTAs could be novel and have not been reported in bread wheat. The markers or genes identified in this study will help reveal the genes controlling the morpho-physiological traits in Ae. tauschii, and thus in bread wheat even if the plant morphology is different.

scholarly journals The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

2017 ◽  
Author(s):  
Aleksey V. Zimin ◽  
Daniela Puiu ◽  
Richard Hall ◽  
Sarah Kingan ◽  
Bernardo J. Clavijo ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Aegilops Tauschii ◽  
Weighted Average ◽  
Wheat Genome ◽  
D Genome ◽  
Genetic Studies ◽  
Final Assembly ◽  
Bread Wheat Genome ◽  
Diploid Ancestor

AbstractCommon bread wheat, Triticum aestivum, has one of the most complex genomes known to science, with 6 copies of each chromosome, enormous numbers of near-identical sequences scattered throughout, and an overall size of more than 15 billion bases. Multiple past attempts to assemble the genome have failed. Here we report the first successful assembly of T. aestivum, using deep sequencing coverage from a combination of short Illumina reads and very long Pacific Biosciences reads. The final assembly contains 15,344,693,583 bases and has a weighted average (N50) contig size of of 232,659 bases. This represents by far the most complete and contiguous assembly of the wheat genome to date, providing a strong foundation for future genetic studies of this important food crop. We also report how we used the recently published genome of Aegilops tauschii, the diploid ancestor of the wheat D genome, to identify 4,179,762,575 bp of T. aestivum that correspond to its D genome components.

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