Genome-Wide Association Analysis of Late Blight Resistance Traits in Potato Germplasm Resources

Abstract Background: Potatoes are dicotyledonous plants of the genus Solanum, family Solanaceae, and contain large amounts of starch, proteins, and trace elements required by the human. Potato late blight is the main disease hindering potato production. In this study, Phytophthora infestans were used to quantify late blight resistance in 284 germplasm resources, and resistance genes were mined through genome-wide association analysis.Results: The results showed that among the 284 potato germplasm resources, 37 showed immunity, 15 were highly resistant to late blight, 30 were moderately resistant to late blight, 107 were moderately susceptible to late blight, and 95 were highly susceptible to late blight. Through screening and filtering, 22,489 high-quality single-nucleotide polymorphisms (SNPs) and indels were obtained. Through population structure analysis and principal-component analysis, 284 germplasm resources were divided into eight subgroups, which was consistent with the results of the phylogenetic tree analysis. The genetic diversity index of the 284 potato germplasm resources was 0.2161, and the differentiation index of each subgroup was 0.0251-0.1489. A mixed linear model was built to perform an association analysis on the diameter of the lesions identified from isolated leaves of potato affected by late blight. The genes within 100 kb of both sides of the obtained significant SNP loci were searched and functionally annotated, and 18 candidate genes were obtained. Twenty-two candidate genes were obtained from the association analysis of disease resistance grade.Conclusions: 284 potato germplasm resources were used to identify for Phytophthora infestans resistance. The potato germplasm resources were divided into 8 subgroups by population structure analysis, and the main differentiation among subgroups was moderate. Candidate genes were mined by genome-wide association analysis.The results of this study provides the foundation for the genetic improvement of potato varieties resistant to late blight.

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Genome-wide association analysis for late blight resistance of potato resources

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2021.04099 ◽

2020 ◽

Vol 47 (2) ◽

pp. 245-261

Author(s):

Wei JIANG ◽

Zhe-Chao PAN ◽

Li-Xian BAO ◽

Fu-Xian ZHOU ◽

Yan-Shan LI ◽

...

Keyword(s):

Late Blight ◽

Association Analysis ◽

Late Blight Resistance ◽

Genome Wide Association ◽

Blight Resistance ◽

Genome Wide Association Analysis ◽

Genome Wide

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Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽

10.3390/genes12050718 ◽

2021 ◽

Vol 12 (5) ◽

pp. 718

Author(s):

Bingxin Meng ◽

Tao Wang ◽

Yi Luo ◽

Deze Xu ◽

Lanzhi Li ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Association Analysis ◽

Genome Wide Association Study ◽

Flag Leaf ◽

Genome Wide Association ◽

Lodging Resistance ◽

Leaf Type ◽

Stem Strength ◽

Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

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Genome-wide association analysis reveals genetic variations and candidate genes associated with growth-related traits and condition factor in Takifugu bimaculatus

Reproduction and Breeding ◽

10.1016/j.repbre.2021.05.001 ◽

2021 ◽

Vol 1 (2) ◽

pp. 89-99

Author(s):

Zhixiong Zhou ◽

Mei Wang ◽

Junyi Yang ◽

Bo Liu ◽

Leibin Li ◽

...

Keyword(s):

Candidate Genes ◽

Association Analysis ◽

Condition Factor ◽

Genetic Variations ◽

Genome Wide Association ◽

Genome Wide Association Analysis ◽

Genome Wide

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Genome-Wide Association Analysis of Fusarium Head Blight Resistance in Chinese Elite Wheat Lines

Frontiers in Plant Science ◽

10.3389/fpls.2020.00206 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 7

Author(s):

Zhanwang Zhu ◽

Ling Chen ◽

Wei Zhang ◽

Lijun Yang ◽

Weiwei Zhu ◽

...

Keyword(s):

Fusarium Head Blight ◽

Association Analysis ◽

Fusarium Head Blight Resistance ◽

Genome Wide Association ◽

Blight Resistance ◽

Head Blight ◽

Genome Wide Association Analysis ◽

Genome Wide ◽

Wheat Lines

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

Frontiers in Genetics ◽

10.3389/fgene.2021.714575 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fang Wang ◽

Meiling Zou ◽

Long Zhao ◽

Zhiqiang Xia ◽

Jian Wang

Keyword(s):

Solanum Tuberosum ◽

Late Blight ◽

Potato Breeding ◽

Genome Wide Association Study ◽

Solanum Tuberosum L ◽

Potato Cultivars ◽

Genome Wide Association ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome

Uncovering the genetic basis and optimizing the late blight tolerance trait in potatoes (Solanum tuberosum L.) are crucial for potato breeding. Late blight disease is one of the most significant diseases hindering potato production. The traits of late blight tolerance were evaluated for 284 potato cultivars to identify loci significantly associated with the late blight tolerance trait. Of all, 37 and 15 were the most tolerant to disease, and 107 and 30 were the most susceptible. A total of 22,489 high-quality single-nucleotide polymorphisms and indels were identified in 284 potato cultivars. All the potato cultivars were clustered into eight subgroups using population structure analysis and principal component analysis, which were consistent with the results of the phylogenetic tree analysis. The average genetic diversity for all 284 potato cultivars was 0.216, and the differentiation index of each subgroup was 0.025–0.149. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about 0.9 kb. A genome-wide association study using a mixed linear model identified 964 loci significantly associated with the late blight tolerance trait. Fourteen candidate genes for late blight tolerance traits were identified, including genes encoding late blight tolerance protein, chitinase 1, cytosolic nucleotide-binding site–leucine-rich repeat tolerance protein, protein kinase, ethylene-responsive transcription factor, and other potential plant tolerance-related proteins. This study provides novel insights into the genetic architecture of late blight tolerance traits and will be helpful for late blight tolerance in potato breeding.

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Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis

Journal of Animal Science ◽

10.1093/jas/skac012 ◽

2022 ◽

Author(s):

Rongrong Ding ◽

Zhanwei Zhuang ◽

Yibin Qiu ◽

Donglin Ruan ◽

Jie Wu ◽

...

Keyword(s):

Candidate Genes ◽

Association Analysis ◽

Large Scale ◽

Major Gene ◽

Gene Set Enrichment Analysis ◽

Genome Wide Association ◽

Backfat Thickness ◽

Lean Meat ◽

Genome Wide Association Analysis ◽

Genome Wide

Abstract Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1 and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1 and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggests that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits, and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

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