Genome-Wide Association Mapping of Late Blight Tolerance Trait in Potato (Solanum tuberosum L.)

Wang, Fang; Zou, Meiling; Zhao, Long; Xia, Zhiqiang; Wang, Jian

doi:10.3389/fgene.2021.714575

Cited by 14 publications

(13 citation statements)

References 42 publications

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“…Among them, mutation and recombination are the most important, along with biological reproduction patterns, genetic drift and selection effects. In this study, the linkage distance of 60 Kb for the tetraploid potatoes is significantly greater than that of 1 Kb in previous studies ( Wang et al., 2021 ). The possible reason for this discrepancy is that we compared all sequencing data to the 48 chromosomes of the reference tetraploid potato, which led to a significant increase in LD.…”

Section: Discussioncontrasting

confidence: 77%

“…At present, the reported studies of potato GWAS are mainly based on haploid reference genome, and few studies of GWAS use tetraploid potato reference genome. Wang et al conducted a pilot GWAS of late blight potatoes and mined 14 candidate genes (Wang et al, 2021). However, the study was limited to the reference genome version, which was selected from diploid DM potato varieties.…”

Section: Introductionmentioning

confidence: 99%

“…Wang et al. conducted a pilot GWAS of late blight potatoes and mined 14 candidate genes ( Wang et al., 2021 ). However, the study was limited to the reference genome version, which was selected from diploid DM potato varieties.…”

Section: Introductionmentioning

confidence: 99%

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Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome

et al. 2023

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Potato is one of the world’s most important food crops, with a time-consuming breeding process. In this study, we performed a genome-wide association (GWAS) analysis of the two important traits of potato tuber shape and eye depth, using the tetraploid potato genome (2n=4x=48) as a reference. A total of 370 potatoes were divided into three subgroups based on the principal component analysis and evolutionary tree analysis. The genetic diversity within subgroups is low (5.18×10-5, 4.36×10-5 and 4.24×10-5). Genome-wide linkage disequilibrium (LD) analysis showed that their LD is about 60 Kb. GWAS analysis identified that 146 significant single nucleotide polymorphism (SNP) loci at Chr01A1:34.44−35.25 Mb and Chr02A1:28.35−28.54 Mb regions are significantly associated with potato tuber shape, and that three candidate genes that might be related to potato tuber traits, PLATZ transcription factor, UTP-glucose-1-phosphate uridylyltransferase and FAR1 DNA-binding domain, are in the association region of Chr02A1. GWAS analysis identified 53 significant SNP loci at Chr05A2: 49.644-50.146 Mb and Chr06A2: 25.866-26.384 Mb regions with robust associations with potato tuber eye depth. Hydrolase and methyltransferases are present in the association region of Chr05A2, and three CYPs are present in the association region of Chr06A2. Our findings suggested that these genes are closely associated with potato tuber shape and eye depth. Our study identified molecular markers and candidate genes for improving tetraploid potato tuber shape and eye depth and provided ideas and insights for tetraploid potato breeding.

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Section: Discussioncontrasting

confidence: 77%

Section: Introductionmentioning

confidence: 99%

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Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome

et al. 2023

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“…Our tip-calibrated coalescent analyses revealed that the time to the most common recent ancestor of that Clade was 32,226 BCE and not 332,580 to 142,980 BCE (Fig. 5B), as previously reported (12,44). Because the same holds true for Clade I, both clades could have coexisted in sympatry 25,000 years later when donkeys were first domesticated (Fig.…”

Section: Donkey Management Involved Inbreeding and Introgression From...supporting

confidence: 81%

The genomic history and global expansion of domestic donkeys

Todd

Tonasso-Calvière

Chauvey

et al. 2022

Science

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Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.

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“…However, the rate of degradation of C. edulis LD was very slow. This method has been successfully applied to other crops, such as M. esculenta Crantz ( Zhang et al, 2018 ) and Solanum tuberosum L. ( Wang et al, 2021 ). A detailed understanding of the demographic structure of a group of members is essential to exclude unnecessary members from the group.…”

Section: Discussionmentioning

confidence: 99%

High-quality reference genome sequences of two Cannaceae species provide insights into the evolution of Cannaceae

Jiang

Zou

et al. 2022

Front. Plant Sci.

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Canna edulis Ker-Gawl and Canna indica L. are species belonging to the Cannaceae family and both have a very high economic value. Here, we aimed to assemble genomes of C. edulis and C. indica at the chromosome level to generate a reference genome for the Cannaceae family. We also comparatively analyzed the genomes of C. edulis and C. indica and examined the molecular mechanisms responsible for the remarkable differences in plant characteristics in C. edulis varieties. Our results indicated that genome-wide duplication events had recently occurred in C. edulis and C. indica. The comparative analysis of the genomes of C. edulis and C. indica revealed that C. edulis exhibited a remarkable level of replication of genes in the starch and sucrose metabolic pathways, especially during sucrose hydrolysis. This finding is consistent with the fact that the starch content of the C. edulis tuber is higher than that of C. indica. Simplified genome re-sequencing revealed the population structure of 241 C. edulis genes, and a genome-wide association study of leaf traits revealed the location of key genes related to leaf color and morphology. These findings extend our understanding of Cannaceade at the molecular level, and provide an effective theoretical basis for further study and utilization of Cannaceae plants.

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Genome-Wide Association Mapping of Late Blight Tolerance Trait in Potato (Solanum tuberosum L.)

Cited by 14 publications

References 42 publications

Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome

Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome

The genomic history and global expansion of domestic donkeys

High-quality reference genome sequences of two Cannaceae species provide insights into the evolution of Cannaceae

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