Genome-wide Identification of the POD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera L)

Xiao, Huilin; Wang, Chaoping; Khan, Nadeem; Chen, Mengxia; Fu, Weihong; Guan, Le; Leng, Xiangpeng

doi:10.21203/rs.2.16423/v1

Cited by 1 publication

(2 citation statements)

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“…Genomic DNA was isolated from leaf samples, paired-end sequencing libraries were constructed, and libraries were sequenced using the Illumina HiSeq 4000 platform with 150-bp paired reads to a target coverage of 30x. The raw sequencing data have been deposited in the Short Read Archive at NCBI under BioProject ID: PRJNA910315 ( 74 ) and the National Genomics Data Center (NGDC) Genome Sequence Archive with BioProject number: PRJCA016655 ( 75 ). We also used Illumina raw reads of 305 samples from previous publications that were downloaded from the Short Read Archive at NCBI.…”

Section: Methodsmentioning

confidence: 99%

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Adaptive and maladaptive introgression in grapevine domestication

Xiao,

Liu,

Wang

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild ( Vitis vinifera ssp. sylvestris ) and cultivated ( V. vinifera ssp. vinifera ) grapes. Based on machine learning–based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.

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Section: Methodsmentioning

confidence: 99%

“…Data (genome sequences; script) have been deposited in NCBI, NGDC and GitHub ( PRJNA910315 ( 74 ); PRJCA016655 ( 75 ); https://github.com/zhouyflab/Grapevine_Adaptive_Maladaptive_Introgression ( 81 )).…”

Section: Data Materials and Software Availabilitymentioning

confidence: 99%