Adaptive and maladaptive introgression in grapevine domestication

Xiao, Hua; Liu, Zhongjie; Wang, Nan; Long, Qiming; Cao, Shuo; Huang, Guizhou; Liu, Wenwen; Peng, Yanling; Riaz, Summaira; Walker, Andrew M.; Gaut, Brandon S.; Zhou, Yongfeng

doi:10.1073/pnas.2222041120

Cited by 30 publications

(25 citation statements)

References 79 publications

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“…5b). For each species, 1 heterozygous SNP was detected every 239-888 bp between haplotypes representing 0.11-0.42% of their assembly (Additional File 1: Table S17) which is consistent with our independent pairwise comparison using NUCmer and reports from literature [16,17].…”

Section: Structural Variants Derived From the Pangenome Graph Topologysupporting

confidence: 88%

A super-pangenome of the North American wild grape species

Cochetel

Minio

García

et al. 2023

Preprint

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Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which were phased and scaffolded at chromosome scale. We generated a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the full resolution of genomic diversity among wild grape species from sequence to gene level. The pangenome graph captured genomic variation between haplotypes within a species and across the different species, and it accurately assessed the similarity of hybrids to their parents. The species selected to build the pangenome ensured a comprehensive representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis (pan-GWAS), we demonstrated the utility of the super-pangenome by effectively mapping short-reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of the adaptive traits from wild relatives, potentially accelerating crop breeding research.

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Section: Structural Variants Derived From the Pangenome Graph Topologysupporting

confidence: 88%

A super-pangenome of the North American wild grape species

Cochetel

Minio

García

et al. 2023

Preprint

Self Cite

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“…SNPs and INDELs represented almost the entirety of the variants detected (99% on average), while translocations or inversions were very few. SNP was the most abundant type of variant with 1 SNP every 238–1159 bp (Additional File 2 : Figure S1) as reported previously for wild grapes species [ 16 , 17 ]. INDELs were more spread with an average distribution six times wider than for the SNPs (1 INDEL every 1652–5030 bp) (Additional File 2 : Figure S1).…”

Section: Resultssupporting

confidence: 71%

A super-pangenome of the North American wild grape species

Cochetel,

Minio,

Guarracino

et al. 2023

Genome Biol

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Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Results Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce’s disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. Conclusions This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.

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“…Currently, in a variety of animals and plants, instances of introgression between wild and domesticated species are gradually being reported. Examples include introgression from markhor to goats [ 9 ], wild relatives to domestic sheep populations (argali to Bashibai, Asiatic mouflon to Grey Shiraz, European mouflon to Caucasian [ 10 ], argali to Tibetan sheep [ 11 , 12 ]), European wild grapes to cultivated wine grapes[ 13 ], wild emmer to modern wheat [ 14 ] and so on.…”

Section: Introductionmentioning

confidence: 99%

Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus)

Zhao,

Wen,

Zhang

et al. 2024

J Animal Sci Biotechnol

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Background Chicken is one of the most numerous and widely distributed species around the world, and many studies support the multiple ancestral origins of domestic chickens. The research regarding the yellow skin phenotype in domestic chickens (regulated by BCO2) likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens. However, beyond the BCO2 gene region, much remains unknown about the introgression from the grey junglefowl into domestic chickens. Therefore, in this study, based on whole-genome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds, we explored the introgression events from the grey junglefowl to domestic chickens. Results We successfully detected introgression regions besides BCO2, including two associated with growth trait (IGFBP2 and TKT), one associated with angiogenesis (TIMP3) and two members of the heat shock protein family (HSPB2 and CRYAB). Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens. Furthermore, we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds, indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained. Additionally, our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens, possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens. Conclusions In summary, our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens, laying the foundation for a deeper understanding of the genetic composition within domestic chickens, and offering new perspectives on the impact of introgression on domestic chickens.

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Adaptive and maladaptive introgression in grapevine domestication

Cited by 30 publications

References 79 publications

A super-pangenome of the North American wild grape species

A super-pangenome of the North American wild grape species

A super-pangenome of the North American wild grape species

Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus)

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