Genomic insights into the evolutionary history and diversification of bulb traits in garlic

Li, Ningyang; Zhang, Xueyu; Sun, Xiaohui; Zhu, Siyuan; Cheng, Yi; Li, Meng; Gao, Song; Zhang, Jiangjiang; Wang, Yanzhou; Yang, Xiai; Chen, Jianrong; Fu, Li; He, Qiaoyun; Zeng, Zheng; Yuan, Xiaoge; Zhou, Zhiman; Ma, Longchuan; Wang, Taotao; Li, Xiang; Liu, Hanqiang; Pan, Yupeng; Zhou, Min; Gao, Chunsheng; Zhou, Gang; Han, Zhenlin; Liu, Shiqi; Su, Jianguang; Cheng, Zhihui; Tian, Shilin; Liu, Touming

doi:10.1186/s13059-022-02756-1

Cited by 12 publications

(27 citation statements)

References 56 publications

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“…The PBS method was proposed to detect a significant change in allele or haplotype frequency along the lineage of one population after it diverged from other populations. Many previous studies demonstrated its efficiency in detecting candidate selection signatures in a target population over short divergence times [ 47 – 49 ]. We finally identified 53,672 candidate selection windows specific to Beijing Black pig and discovered that DNAJC6 and RUFY4 are related to meat quality traits.…”

Section: Discussionmentioning

confidence: 99%

Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed

Du,

Liu,

et al. 2024

BMC Genomics

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Background The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown. Results Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness. Conclusions Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.

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Section: Discussionmentioning

confidence: 99%

Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed

Du,

Liu,

et al. 2024

BMC Genomics

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“…Similarly, in the elite yield trials evaluation experiment of four groups of wheat breeding lines including this population in 2019, 78 606 markers were strictly filtered, resulting in 16 072 GBS markers showing the effect of high coverage on trait predictability for subsequent trials [ 70 ]. The high-quality SNPs obtained from 230 garlic germplasms screened by GBS technology were sequenced to infer population structure, and four main groups were found in garlic germplasm [ 71 ]. GBS analysis of 190 young pepper leaves produced only 4083 effective SNPs, which elucidated the origin of Spanish regional varieties and the path of pepper evolution [ 72 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study of 23 flowering phenology traits and 4 floral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate flowering time

Guo

Wang³

et al. 2022

Horticulture Research

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Tree peony is a unique traditional flower in China, with large, fragrant, and colorful flowers. However, a relatively short and concentrated flowering period limits the applications and production of tree peony. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of flowering phenology traits and ornamental phenotypes in tree peony. A diverse panel of 451 tree peony accessions was phenotyped for 23 flowering phenology traits and 4 floral agronomic traits over three years. Genotyping by sequencing (GBS) was used to obtain a large number of genome-wide SNPs (107 050) for the panel genotypes, and 1047 candidate genes were identified by association mapping. Eighty-two related genes were observed during at least two years for flowering, and 7 SNPs repeatedly identified for multiple flowering phenology traits over multiple years were highly significantly associated with 5 genes known to regulate flowering time. We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of flower bud differentiation and flowering time in tree peony. This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony. The results expand our understanding of flowering time control in perennial woody plants. Identification of markers closely related to these flowering phenology traits can be used in tree peony breeding programs for important agronomic traits.

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“…Only SNPs with MAF ≥ 0.01 [ 70 – 72 ] and missing rate ≤ 0.1 in a population were used for GWAS. Efficient Mixed-Model Association eXpedited program (EMMAx) was used for GWAS analysis [ 73 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

He,

Zhang,

Shi

et al. 2024

Genome Biol

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Background Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. Results Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. Conclusions This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.

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Genomic insights into the evolutionary history and diversification of bulb traits in garlic

Cited by 12 publications

References 56 publications

Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed

Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed

Genome-wide association study of 23 flowering phenology traits and 4 floral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate flowering time

Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

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