Effects of demographic history on recombination hotspots in soybean

The Plant Journal, Journal Year: 2024, Volume and Issue: 119(2), P. 1030 - 1038

Published: May 23, 2024

SUMMARY Recombination is the primary mechanism underlying genetic improvement in populations and allows plant breeders to create new allelic combinations for agronomic improvement. Soybean [ Glycine max (L.) Merr.] has gone through multiple bottlenecks that have significantly affected its diversity, linkage disequilibrium, altered allele frequencies. To investigate impact of on recombination hotspots soybeans, historical was studied three soybean populations. The were wild soja (Sieb. Zucc.)], landraces, North American elite cultivars been genotyped with SoySNP50K BeadChip. While each population after a bottleneck had an increased average haplotype block size, they did not significant difference number between population. Instead, increase observed size likely due elimination individuals contained at which decreased rate hotspot bottleneck. Conversely, heterochromatic DNA compared euchromatic different but rate. Previously identified genomic motifs associated also found suggesting common mechanism. This characterization soybeans provides further insights into effect selection hotspots.

Language: Английский

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Individual variation in meiotic crossover positioning, rate and interference are associated with distinct genetic processes in domestic pigs

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 24, 2024

Abstract Meiotic crossovers are essential for proper chromosome segregation, and provide an important mechanism adaptation through linking beneficial alleles purging deleterious mutations. However, can also break apart themselves a source of new mutations within the genome. The rate distribution shows huge variation both between chromosomes, individuals species, yet molecular evolutionary causes consequences this remain poorly understood. A key step in understanding is to understand genetic architecture how many occur, where they interfere, as allows us identify degree which these factors governed by common or distinct processes. Here, we investigate individual crossover count, interference (ν), positioning measured intra-chromosomal allelic shuffling distance telomere (Mb), large genotyped breeding population domestic pigs. Using measures from 82,474 gametes 4,704 mothers 271 fathers, show that traits heritable each sex (h 2 = 0.03 - 0.11), with exception male interference. Crossover count have strongly shared females, mostly driven variants at RNF212 . Female mediated MEI4 , PRDM9 SYCP2 We tentative associations genomic regions corresponding CTCF REC114/REC8/CCNB1IP1 (crossover count), ZCWPW1 ZCWPW2 positioning). Our results female pigs capacity evolve somewhat independently our dataset.

Language: Английский

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A catalogue of recombination coldspots in interspecific tomato hybrids

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(7), P. e1011336 - e1011336

Published: July 1, 2024

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially crosses between divergent genomes, limiting the combinations desirable alleles. Here, we used pooled-pollen sequencing to build map recombinant non-recombinant tomato five commonly introgressive breeding. We detected hybrid-specific coldspots that underscore role structural variations modifying patterns maintaining genetic linkage interspecific crosses. Crossover show strong association TE superfamilies exhibiting differentially accessible chromatin somatic cells. About two-thirds genome conserved coldspots, located mostly pericentromeres enriched retrotransposons. The also harbor genes associated agronomic stress resistance, revealing undesired consequences drag possible barriers presented examples can potentially be resolved pairing other species. Overall, this catalogue will help breeders better understand crossover localization make informed decisions on generating new varieties.

Language: Английский

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Mixed outcomes in recombination rates after domestication: Revisiting theory and data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 9, 2024

Abstract The process of domestication has altered many phenotypes. Selection on these phenotypes long been hypothesized to indirectly select for increases in recombination rate. This hypothesis is consistent with theory the evolution rate, but empirical support unclear. We review relevant theory, lab-based experiments, and data comparing rates wild progenitors their domesticated counterparts. utilize population sequencing a deep learning method infer genome-wide new comparisons chicken/red junglefowl, sheep/mouflon, goat/bezoar. find evidence increased domestic goats compared bezoars, more mixed results chicken, generally decreased sheep mouflon. Our add growing body literature plants animals that finds no an increase domestication.

Language: Английский

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Auxin-driven ecophysiological diversification of leaves in domesticated tomato

PLANT PHYSIOLOGY, Journal Year: 2022, Volume and Issue: 190(1), P. 113 - 126

Published: May 27, 2022

Abstract Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalize the parenchyma, whereas homobaric do not. The presence of BSEs affects leaf hydraulics and photosynthetic rate. tomato (Solanum lycopersicum) obscuravenosa (obv) mutant lacks BSEs. Here, we identify obv gene causative mutation, a nonsynonymous amino acid change disrupts C2H2 zinc finger motif in putative transcription factor. This mutation exists as polymorphism natural range wild tomatoes but has increased frequency domesticated tomatoes, suggesting latter diversified into heterobaric types. displays reduced vein density, hydraulic conductance assimilation We show these other pleiotropic effects on plant development, including changes insertion angle, margin serration, minor fruit shape, are controlled by OBV via auxin signaling. Loss function transcriptional regulator AUXIN RESPONSE FACTOR 4 (ARF4) also results defective BSE revealing an additional component genetic module controlling aspects development important for ecological adaptation subject to breeding selection.

Language: Английский

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Recruiting Distant Hybridization for Reshaping Meiotic Recombination

Plant Breeding and Biotechnology, Journal Year: 2023, Volume and Issue: 11(3), P. 168 - 184

Published: Aug. 31, 2023

Gene introgression that involves the transfer of favorable allelic diversity for broadening genetic base breeding materials is a powerful 'toolkit' creating novel combinations during plant sexual reproduction.It key factor playing an important role in schemes by reintroducing variation at selective sweeps or desirable traits required development new varieties.Meiosis specialized cell division not only enables sexually reproducing organisms to reduce their genomic constituent half, also provides indefinitely reshuffling parental makeup.Crossing over takes place prophase-I facilitates meiotically exchange between homolog pairs as well accurate segregations.It tightly modulated and many intrinsic factors extrinsic agents are associated with regulation process, however, modulation meiosis possible.Although, advanced approaches such CRIPR/Cas Virus-Induced gene Silencing (VIGS) have opened horizons manipulation meiotic recombination, distant hybridization could effectively influence frequency distribution homologous (HR) particularly homoeologous recombination (HeR).In this review, we provide brief overview recent advances mechanisms HR HeR employing hybridization.

Language: Английский

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Alternative Modes of Introgression-Mediated Selection Shaped Crop Adaptation to Novel Climates

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(8)

Published: July 21, 2022

Abstract Recent plant genomic studies provide fine-grained details on the evolutionary consequences of adaptive introgression during crop domestication. Modern approaches and analytical methods now make it possible to better separate signal from demographic thus providing a more comprehensive complex picture role in local adaptation. Adaptive has been fundamental for expansion involved patterns gene flow. In addition new favorable alleles large effect, early stages domestication also increased allelic diversity at loci. Previous have largely underestimated effect such following introgression. wheat, potato, maize, grapevine, ryegrass show that multiple genes, as yet unknown effectiveness purifying selection, promoted disruptive or fluctuating selection cultivars landraces. Historical processes associated with wild relatives an instructive analog adaptation current climate change offer avenues breeding research are expected be instrumental strengthening food security coming years.

Language: Английский

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Chromosome-level genome and recombination map of the male buffalo

GigaScience, Journal Year: 2022, Volume and Issue: 12

Published: Dec. 28, 2022

Abstract Background The swamp buffalo (Bubalus bubalis carabanesis) is an economically important livestock supplying milk, meat, leather, and draft power. Several female genomes have been available, but the lack of high-quality male hinders studies on chromosome evolution, especially Y, as well meiotic recombination. Results Here, a chromosome-level genome with contig N50 72.2 Mb fine-scale recombination map were reported. We found that transposable elements (TEs) structural variants (SVs) may contribute to evolution by influencing adjacent gene expression. further pseudoautosomal region (PAR) Y subject stronger purification selection. showed there 2 obvious hotspots 8, genes around them mainly related tooth development, which helped enhance adaption inferior feed. Among several genomic features, TE density has strongest correlation rates. Moreover, subfamily, SINE/tRNA, likely play role in driving into SVs. Conclusions sperm sequencing will facilitate understanding functional research.

Language: Английский

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Rapid evolution of fine-scale recombination during domestication

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 6, 2024

ABSTRACT Recombination serves as a central force driving the evolution of genomic diversity in sexually reproducing organisms. Despite its fundamental role, evolutionary dynamics recombination rates remain largely elusive. The domestication animals, characterized by dynamic selective pressures, provides unique lens through which to investigate these phenomena. Here, we constructed fine-scale map using whole-genome data from domestic chickens, including both contemporary commercial breeds and their wild progenitor, Red Junglefowl (RJF). Our analysis reveals rapid landscape within between chicken populations, find that average rate decreased during domestication. Remarkably, this trend is further corroborated re-analysis genomes several species ducks, goats, pigs, sheep. Contrary hypothesis leads an increase rates, our results provide no support for such scenario. We suggest low beneficial maintaining uniform stable phenotypes inbreeding. Furthermore, significant variation hotspots across particularly pronounced despite recent divergence. turnover coldspots appears be closely linked sweeps. Interestingly, contrast prevailing observations most species, long-term inbreeding negative correlation frequency introgressed ancestry other RJF subspecies. insights into complex interplay forces shaping recombination.

Language: Английский

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Analysis of the winter oilseed rape recombination landscape suggests maternal–paternal bias

Genome, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 21, 2024

Recombination, the reciprocal exchange of DNA between homologous chromosomes, is a mandatory step necessary for meiosis progression. Crossovers chromosomes generate new combinations alleles and maintain genetic diversity. Due to genetic, epigenetic, environmental factors, recombination landscape highly heterogeneous along it also differs populations sexes. Here, we investigated characteristics across 19 model allopolyploid crop species oilseed rape ( Brassica napus L.), using two unique multiparental derived from genetically divergent founder pools, each which comprised 50 diverse accessions. A fully balanced, pairwise chain-crossing scheme was utilized create populations. total 3213 individuals, spanning five successive generations, were genotyped 15K SNP array. We observed uneven distribution with some genomic regions undergoing substantially more frequent in both In populations, maternal events than paternal recombination. This study provides insight into at chromosomal level reveals maternal–paternal bias number implications breeding.

Language: Английский

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