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Sharma SK, McLean K, Hedley PE, Dale F, Daniels S, Bryan GJ. Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:180. [PMID: 38980417 DOI: 10.1007/s00122-024-04651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/10/2024] [Indexed: 07/10/2024]
Abstract
KEY MESSAGE De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over 'fixed' SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker-trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a 'fixed' SNP Infinium array platform and a 'flexible and open' genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL 'hotspots' for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.
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Affiliation(s)
- Sanjeev Kumar Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Karen McLean
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Finlay Dale
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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Zhao L, Zou M, Deng K, Xia C, Jiang S, Zhang C, Ma Y, Dong X, He M, Na T, Wang J, Xia Z, Wang F. Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome. FRONTIERS IN PLANT SCIENCE 2023; 14:1080666. [PMID: 37056497 PMCID: PMC10086151 DOI: 10.3389/fpls.2023.1080666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
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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Affiliation(s)
- Long Zhao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Meiling Zou
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Ke Deng
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Chengcai Xia
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Sirong Jiang
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Chenji Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yongzhen Ma
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Xiaorui Dong
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Miaohua He
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Tiancang Na
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, China
- Qinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Jian Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, China
- Qinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Zhiqiang Xia
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Fang Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, China
- Qinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
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3
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Huang W, Dong J, Zhao X, Zhao Z, Li C, Li J, Song B. QTL analysis of tuber shape in a diploid potato population. FRONTIERS IN PLANT SCIENCE 2022; 13:1046287. [PMID: 36438140 PMCID: PMC9685338 DOI: 10.3389/fpls.2022.1046287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Tuber shape is one of the most important traits for potato breeding. Since poor or irregular shape increases the difficulty of handling and processing, researching the inheritance of potato tuber shape for potato breeding is highly important. To efficiently identify QTL for tuber shape, a diploid potato population (PM7) was generated by self-pollinated M6 (S. chacoense). A QTL TScha6 for tuber shape was identified by the QTL-seq approach at 50.91-59.93 Mb on chromosome 6 in the potato DM reference genome. To confirm TScha6, four SSR and twenty CAPS markers around the QTL were developed and the TScha6 was narrowed down to an interval of ~ 1.85 Mb. The CAPS marker C6-58.27_665 linked to TScha6 was then used to screen 86 potato cultivars and advanced breeding lines. The tuber length/width (LW) ratio was significantly correlated with the presence/absence of C6-58.27_665, and the correlation coefficient was r = 0.55 (p < 0.01). These results showed that C6-58.27_665 could be applied in marker-assisted selection (MAS) for tuber shape breeding in the future. Our research sets the important stage for the future cloning of the tuber shape gene and utilities of the marker in the breeding program.
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Affiliation(s)
- Wei Huang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
- Forestry and Fruit Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Jianke Dong
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xijuan Zhao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhiyuan Zhao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chunyan Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jingcai Li
- College of Biology and Agricultural Resources, Huanggang Normal University/Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, Hubei, China
| | - Botao Song
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
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Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato. Int J Mol Sci 2022; 23:ijms23031470. [PMID: 35163389 PMCID: PMC8836246 DOI: 10.3390/ijms23031470] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 12/10/2022] Open
Abstract
Tuber shape is one of the most important quality traits in potato appearance. Since poor or irregular shape results in higher costs for processing and influences the consumers’ willingness to purchase, breeding for shape uniformity and shallow eye depth is highly important. Previous studies showed that the major round tuber shape controlling locus, the Ro locus, is located on chromosome 10. However, fine mapping and cloning of tuber shape genes have not been reported. In this study, the analyses of tissue sectioning and transcriptome sequencing showed that the developmental differences between round and elongated tuber shapes begin as early as the hook stage of the stolon. To fine map tuber shape genes, a high-density genetic linkage map of the Ro region on chromosome 10 based on a diploid segregating population was constructed. The total length of the genetic linkage map was 25.8 cM and the average marker interval was 1.98 cM. Combined with phenotypic data collected from 2014 to 2017, one major quantitative trait locus (QTL) for tuber shape was identified, which explained 61.7–72.9% of the tuber shape variation. Through the results of genotyping and phenotypic investigation of recombinant individuals, Ro was fine mapped in a 193.43 kb interval, which contained 18 genes. Five candidate genes were preliminarily predicted based on tissue sections and transcriptome sequencing. This study provides an important basis for cloning Ro gene(s).
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Totsky IV, Rozanova IV, Safonova AD, Batov AS, Gureeva YA, Kochetov AV, Khlestkina EK. Genomic regions of Solanum tuberosum L. associated with the tuber eye depth. Vavilovskii Zhurnal Genet Selektsii 2020; 24:465-473. [PMID: 33659830 PMCID: PMC7716516 DOI: 10.18699/vj20.638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https://plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth.
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Affiliation(s)
- I V Totsky
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Rozanova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - A D Safonova
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Batov
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu A Gureeva
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Kochetov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E K Khlestkina
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Zia MAB, Demirel U, Nadeem MA, Çaliskan ME. Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1003-1020. [PMID: 32377049 PMCID: PMC7196606 DOI: 10.1007/s12298-020-00785-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 02/01/2020] [Accepted: 02/21/2020] [Indexed: 05/22/2023]
Abstract
Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Niğde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r2 value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.
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Affiliation(s)
- Muhammad Abu Bakar Zia
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
- College of Agriculture, Bolu Abant Izzet Baysal University, Bahadur Sub Campus Layyah, Pakistan
| | - Ufuk Demirel
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
| | - Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Science, Bahauddin Zakariya University, 14000 Bolu, Turkey
| | - Mehmet Emin Çaliskan
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
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Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato. Genetics 2019; 212:317-332. [PMID: 30885982 DOI: 10.1534/genetics.119.302036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Deconvolution of the genetic architecture underlying yield is critical for understanding bases of genetic gain in species of agronomic importance. To dissect the genetic components of yield in potato, we adopted a reference-based recombination map composed of four segregating alleles from an interspecific pseudotestcross F1 potato population (n = 90). Approximately 1.5 million short nucleotide variants were utilized during map construction, resulting in unprecedented resolution for an F1 population, estimated by a median bin length of 146 kb and 11 genes per bin. Regression models uncovered 14 quantitative trait loci (QTL) underpinning yield, average tuber weight, and tubers produced per plant in a population exhibiting a striking 332% average midparent-value heterosis. Nearly 80% of yield-associated QTL were epistatic, and contained between 0 and 44 annotated genes. We found that approximately one-half of epistatic QTL overlap regions of residual heterozygosity identified in the inbred parental parent (M6). Genomic regions recalcitrant to inbreeding were associated with an increased density of genes, many of which demonstrated signatures of selection and floral tissue specificity. Dissection of the genome-wide additive and dominance values for yield and yield components indicated a widespread prevalence of dominance contributions in this population, enriched at QTL and regions of residual heterozygosity. Finally, the effects of short nucleotide variants and patterns of gene expression were determined for all genes underlying yield-associated QTL, exposing several promising candidate genes for future investigation.
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Image-based automated potato tuber shape evaluation. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2018. [DOI: 10.1007/s11694-017-9683-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Hara-Skrzypiec A, Śliwka J, Jakuczun H, Zimnoch-Guzowska E. QTL for tuber morphology traits in diploid potato. J Appl Genet 2018; 59:123-132. [PMID: 29492845 PMCID: PMC5895667 DOI: 10.1007/s13353-018-0433-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 11/24/2022]
Abstract
A diploid, potato mapping population consisting of 149 individuals was assessed in three consecutive years for important agronomic and quality traits: tuber shape, regularity of tuber shape, eye depth, mean tuber weight, and tuber flesh color. Analysis of variance showed that the genotype had the largest influence on the phenotypic scores but effect of the genotype × year interactions was also strong. Using this data and an existing genetic map, a quantitative trait loci (QTL) analysis was conducted. From four to seven QTL were detected for each trait except tuber flesh color, which was determined by a major QTL on chromosome III explaining 76.8% of the trait variance. Additionally, a minor QTL for flesh color was localized on chromosome II. For the other traits, significant QTL were detected: for tuber shape on chromosome X, for regularity of tuber shape on chromosome III, for eye depth on chromosome IV, and for tuber weight on chromosome I. Some detected QTL confirmed previous studies, but new ones were also identified.
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Affiliation(s)
- Agnieszka Hara-Skrzypiec
- Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| | - J Śliwka
- Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - H Jakuczun
- Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - E Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa 19, 05-831, Młochów, Poland
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Manrique-Carpintero NC, Coombs JJ, Pham GM, Laimbeer FPE, Braz GT, Jiang J, Veilleux RE, Buell CR, Douches DS. Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits. FRONTIERS IN PLANT SCIENCE 2018; 9:944. [PMID: 30018631 PMCID: PMC6037889 DOI: 10.3389/fpls.2018.00944] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/12/2018] [Indexed: 05/18/2023]
Abstract
The cultivated potato (Solanum tuberosum) has a complex genetic structure due to its autotetraploidy and vegetative propagation which leads to accumulation of mutations and a highly heterozygous genome. A high degree of heterozygosity has been considered to be the main driver of fitness and agronomic trait performance in potato improvement efforts, which is negatively impacted by genetic load. To understand the genetic landscape of cultivated potato, we constructed a gynogenic dihaploid (2n = 2x = 24) population from cv. Superior, prior to development of a high-density genetic map containing 12,753 single nucleotide polymorphisms (SNPs). Common quantitative trait loci (QTL) were identified for tuber traits, vigor and height on chromosomes 2, 4, 7, and 10, while specific QTL for number of inflorescences per plant, and tuber shape were present on chromosomes 4, 6, 10, and 11. Simplex rather than duplex loci were mainly associated with traits. In general, the Q allele (main effect) detected in one or two homologous chromosomes was associated with lower mean trait values suggesting the importance of dosage allelic effects, and the presence of up to two undesired alleles in the QTL region. Loss of heterozygosity has been associated with a lower rate of fitness, yet no correlation between the percent heterozygosity and increased fitness or agronomic performance was observed. Based upon linkage phase, we reconstructed the four homologous chromosome haplotypes of cv. Superior. revealing heterogeneity throughout the genome yet nearly duplicate haplotypes occurring among the homologs of particular chromosomes. These results suggest that the potentially deleterious mutations associated with genetic load in tetraploid potato could be mitigated by multiple loci which is consistent with the theory that epistasis complicates the identification of associations between markers and phenotypic performance.
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Affiliation(s)
- Norma C. Manrique-Carpintero
- Potato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Joseph J. Coombs
- Potato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Gina M. Pham
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | | | - Guilherme T. Braz
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | | | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
| | - David S. Douches
- Potato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- *Correspondence: David S. Douches
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Katsarou K, Wu Y, Zhang R, Bonar N, Morris J, Hedley PE, Bryan GJ, Kalantidis K, Hornyik C. Insight on Genes Affecting Tuber Development in Potato upon Potato spindle tuber viroid (PSTVd) Infection. PLoS One 2016; 11:e0150711. [PMID: 26937634 PMCID: PMC4777548 DOI: 10.1371/journal.pone.0150711] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/18/2016] [Indexed: 01/12/2023] Open
Abstract
Potato (Solanum tuberosum L) is a natural host of Potato spindle tuber viroid (PSTVd) which can cause characteristic symptoms on developing plants including stunting phenotype and distortion of leaves and tubers. PSTVd is the type species of the family Pospiviroidae, and can replicate in the nucleus and move systemically throughout the plant. It is not well understood how the viroid can affect host genes for successful invasion and which genes show altered expression levels upon infection. Our primary focus in this study is the identification of genes which can affect tuber formation since viroid infection can strongly influence tuber development and especially tuber shape. In this study, we used a large-scale method to identify differentially expressed genes in potato. We have identified defence, stress and sugar metabolism related genes having altered expression levels upon infection. Additionally, hormone pathway related genes showed significant up- or down-regulation. DWARF1/DIMINUTO, Gibberellin 7-oxidase and BEL5 transcripts were identified and validated showing differential expression in viroid infected tissues. Our study suggests that gibberellin and brassinosteroid pathways have a possible role in tuber development upon PSTVd infection.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Yun Wu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Nicola Bonar
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- * E-mail: (KK); (CH)
| | - Csaba Hornyik
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
- * E-mail: (KK); (CH)
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