Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

Alicia N. Massa; Norma C. Manrique-Carpintero; Joseph Coombs; Kathleen G. Haynes; Paul C. Bethke; Tina L. Brandt; Sanjay K. Gupta; G. Craig Yencho; Richard G. Novy; David S. Douches

doi:10.1186/s12863-018-0672-1

Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

Alicia N. Massa, Norma C. Manrique-Carpintero, Joseph Coombs, Kathleen G. Haynes, Paul C. Bethke, Tina L. Brandt, Sanjay K. Gupta, G. Craig Yencho, Richard G. Novy, David S. Douches

Soil, Water, and Climate

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Abstract

Background: Genome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance. Results: In this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with ‘Premier Russet’ contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.). Conclusions: Linkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control.

Original language	English (US)
Article number	87
Journal	BMC genetics
Volume	19
Issue number	1
DOIs	https://doi.org/10.1186/s12863-018-0672-1
State	Published - Sep 21 2018

Bibliographical note

Funding Information:
This work was supported by funds from the U.S. Department of Agriculture, National Institute of Food and Agriculture, Agriculture and Food Research Initiative Plant Breeding, Genetics, and Genome grant 2009–85606-05673.

Publisher Copyright:
© 2018 Author(s).

Keywords

Potato
Quantitative trait locus
Single nucleotide polymorphism
Solanum tuberosum
Tuber processing quality
Vine maturity

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title = "Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato",

abstract = "Background: Genome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance. Results: In this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with {\textquoteleft}Premier Russet{\textquoteright} contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.). Conclusions: Linkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control.",

keywords = "Potato, Quantitative trait locus, Single nucleotide polymorphism, Solanum tuberosum, Tuber processing quality, Vine maturity",

author = "Massa, {Alicia N.} and Manrique-Carpintero, {Norma C.} and Joseph Coombs and Haynes, {Kathleen G.} and Bethke, {Paul C.} and Brandt, {Tina L.} and Gupta, {Sanjay K.} and Yencho, {G. Craig} and Novy, {Richard G.} and Douches, {David S.}",

note = "Funding Information: This work was supported by funds from the U.S. Department of Agriculture, National Institute of Food and Agriculture, Agriculture and Food Research Initiative Plant Breeding, Genetics, and Genome grant 2009–85606-05673. Publisher Copyright: {\textcopyright} 2018 Author(s).",

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AU - Massa, Alicia N.

AU - Manrique-Carpintero, Norma C.

AU - Coombs, Joseph

AU - Haynes, Kathleen G.

AU - Bethke, Paul C.

AU - Brandt, Tina L.

AU - Gupta, Sanjay K.

AU - Yencho, G. Craig

AU - Novy, Richard G.

AU - Douches, David S.

N1 - Funding Information: This work was supported by funds from the U.S. Department of Agriculture, National Institute of Food and Agriculture, Agriculture and Food Research Initiative Plant Breeding, Genetics, and Genome grant 2009–85606-05673. Publisher Copyright: © 2018 Author(s).

PY - 2018/9/21

Y1 - 2018/9/21

N2 - Background: Genome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance. Results: In this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with ‘Premier Russet’ contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.). Conclusions: Linkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control.

AB - Background: Genome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance. Results: In this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with ‘Premier Russet’ contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.). Conclusions: Linkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control.

KW - Potato

KW - Quantitative trait locus

KW - Single nucleotide polymorphism

KW - Solanum tuberosum

KW - Tuber processing quality

KW - Vine maturity

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Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

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