Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits

Manrique-Carpintero, Norma C.; Coombs, Joseph; Pham, Gina M.; Laimbeer, F. Parker E.; Braz, Guilherme Tomaz; Jiang, Jiming; Veilleux, Richard E.; Buell, C. Robin; Douches, David S.

doi:10.3389/fpls.2018.00944

Cited by 33 publications

(49 citation statements)

References 62 publications

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“…In this study, for the first time, a high-throughput simplified 2b-RAD sequencing technique approach was used to identify and mark genetic segments for complex quantitative traits in potatoes. Segments with a large difference in specific tags were identified in chromosome 4 and 5, and further tag validation showed that the genetic segment in chromosome 5 is associated with the early maturity trait, which is consistent with previous studies [2,3,4,8,9,10,18]. …”

Section: Discussionsupporting

confidence: 90%

“…Later, it was found that the major QTLs that control maturity in chromosome 5 were closely related to the QTLs controlling late blight resistance, but they were independent from each other and closely linked to the GP21 marker [7]. Tetraploid potatoes (2 n = 4× = 48) are highly heterozygous and have a high frequency of genetic recombination and a complicated genetic ratios [8]. It is much more difficult to conduct genetic analysis with tetraploid material than with diploid potatoes.…”

Section: Introductionmentioning

confidence: 99%

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Mapping and QTL Analysis of Early-Maturity Traits in Tetraploid Potato (Solanum tuberosum L.)

Duan

et al. 2018

IJMS

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Early maturity is one of the most important agronomical traits in potato breeding. To identify the DNA segment that codes for early maturity, a tetraploid potato segregation population of “Zhongshu 19” × “Zhongshu 3” was genetically analyzed, using a combination of high throughput simplified genome sequencing (2b-RAD) and bulked segregant analysis (BSA). The DNA segment related to the early-maturity trait was identified at the 3.7~4.2 Mb locus on the short arm of chromosome 5. Eight molecular markers were developed, of which five were closely linked to the early-maturity trait loci. Additionally, 42 simple sequence repeats (SSR) markers were constructed based on the reference sequence of Solanum tuberosum group Phureja DM1-3 516 R44 (DM). Using the TetraploidMap software, the linkage map of chromosome 5 was constructed with 50 markers. The total map length was 172 centiMorgan (cM), with an average genetic distance of 3.44 cM. Correlating molecular and phenotypic data of the segregating population, the mapped Quantitative Trait Loci (QTL) on the short arm of chromosome 5 contributed to 33.55% of the early-maturity phenotype. The early-maturity QTL was located at 84 cM, flanked by the SSR5-85-1 and SCAR5-8 markers. The QTL was fine-mapped to 471 kb. Using DNA sequence annotation, 34 genes were identified in this region, 12 of them with unknown function. Among the other 22 annotated genes, E3 ubiquitin ligase gene PUB14 could be related to maturity and regulation of tuber formation. The constructed QTL map is a useful basic tool for the cloning of early-maturity related genes in tetraploid potatoes.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Mapping and QTL Analysis of Early-Maturity Traits in Tetraploid Potato (Solanum tuberosum L.)

Duan

et al. 2018

IJMS

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“…Combined with the availability of statistical tools that enable the utilization of allele dosage information (i.e., the number of copies of each allele at a given polymorphic locus), it is now possible to significantly increase the power of SNP information to detect recombination events and to incorporate this information into QTL mapping [ 5 – 7 ]. To date, this approach has been successfully used to detect novel QTLs and candidate SNPs associated with late blight resistance [ 4 , 8 ], internal heat necrosis [ 9 ], Potato virus Y [ 10 ], and agronomic traits [ 11 ], but largely unexplored for studying processing quality and other high-value traits with complex inheritance.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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BackgroundGenome-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.ResultsIn 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.).ConclusionsLinkage 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.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0672-1) contains supplementary material, which is available to authorized users.

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“…This is because one individual can carry more than two alleles at a locus and these alleles can be present in different dosages. The information about allele dosage is important for genetic studies, because a wide range of allelic combinations can occur at a locus that can result in different phenotypes [1][2][3][4] Similar to diploids, SNP genotyping has become state-of-art in polyploids. High-throughput genotyping often is performed by the use of conventional SNP arrays [5][6][7][8][9][10].…”

Section: Introductionmentioning

confidence: 99%

Micro-haplotyping in polyploids using massively parallel amplicon sequencing

Geest

Willemsen²,

Gujjula

et al. 2020

Preprint

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Background Haplotyping in polyploids is a very relevant but challenging task. Most methods based on short-read technologies require haplotype assembly, which is error-prone and computationally intensive. However, most (auto)polyploids have high SNP densities. Therefore, haplotyping could already be done in regions of a size that can be entirely covered by reads generated by current short-read sequencing techniques. Here, we used a method that enables massively parallel amplicon sequencing in order to generate such micro-haplotypes in autotetraploid potato and autohexaploid chrysanthemum. Results For potato, we generated 79 million reads to sequence 412 regions in 96 samples. The average region size was 154 base-pairs. On average, we found 2.4 haplotypes per locus per individual. For chrysanthemum, we generated a similar amount of reads to sequence 940 regions in 92 samples. The average region size here was 171 base-pairs. On average, 2.7 haplotypes per locus per individual were found. Concordance with dosage data based on SNP-arrays was up to 96.8% in potato and 94.2% in chrysanthemum. Conclusions Interpretation of genotyping data generated with next-generation sequencing can be challenging in polyploids, because estimation of allele dosages is often a requisite. Taking advantage of high SNP densities in many autopolyploids we show that massively parallel amplicon sequencing can generate high-quality data with high information content. This has a broad range of applications, including linkage mapping, diversity studies, and genomic selection.

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Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits

Cited by 33 publications

References 62 publications

Mapping and QTL Analysis of Early-Maturity Traits in Tetraploid Potato (Solanum tuberosum L.)

Mapping and QTL Analysis of Early-Maturity Traits in Tetraploid Potato (Solanum tuberosum L.)

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

Micro-haplotyping in polyploids using massively parallel amplicon sequencing

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