Inheritance and genetic mapping of tuber eye depth in cultivated diploid potatoes

Li, Xiuqing; Jong, H. De; Jong, Darlene M. De; Jong, Walter S. De

doi:10.1007/s00122-005-1927-6

Cited by 52 publications

(58 citation statements)

References 19 publications

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“…In contrast, overall nucleotide diversity was reduced on chromosome 10. Some of the most conserved genes in the dataset are located near the position of the skin colour, tuber shape and eye depth QTL on chromosome 10 [65]–[67]. An eye-catching difference between commercial western germplasm and Latin American land races are the highly variable tuber shapes and anthocyanin pigmentation patterns in tuber skin and flesh.…”

Section: Discussionmentioning

confidence: 99%

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

Uitdewilligen

Wolters

D’hoop³

et al. 2013

PLoS ONE

326

368

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Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1–3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (π = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ∼60–80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and alleles strongly influencing maturity and flesh colour were identified.

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Section: Discussionmentioning

confidence: 99%

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

Uitdewilligen

Wolters

D’hoop³

et al. 2013

PLoS ONE

326

368

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“…Potato diploid clone 11379-03 (DC) (essentially a S. tuberosum L.) [32] was used in this study. DC was derived from a number of crosses between different subspecies of the S. tuberosum group ( S. stenotomum , S. phureja , and S. tuberosum ssp.…”

Section: Methodsmentioning

confidence: 99%

Selective Loss of Cysteine Residues and Disulphide Bonds in a Potato Proteinase Inhibitor II Family

Zhang

Donnelly

2011

PLoS ONE

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Disulphide bonds between cysteine residues in proteins play a key role in protein folding, stability, and function. Loss of a disulphide bond is often associated with functional differentiation of the protein. The evolution of disulphide bonds is still actively debated; analysis of naturally occurring variants can promote understanding of the protein evolutionary process. One of the disulphide bond-containing protein families is the potato proteinase inhibitor II (PI-II, or Pin2, for short) superfamily, which is found in most solanaceous plants and participates in plant development, stress response, and defence. Each PI-II domain contains eight cysteine residues (8C), and two similar PI-II domains form a functional protein that has eight disulphide bonds and two non-identical reaction centres. It is still unclear which patterns and processes affect cysteine residue loss in PI-II. Through cDNA sequencing and data mining, we found six natural variants missing cysteine residues involved in one or two disulphide bonds at the first reaction centre. We named these variants Pi7C and Pi6C for the proteins missing one or two pairs of cysteine residues, respectively. This PI-II-7C/6C family was found exclusively in potato. The missing cysteine residues were in bonding pairs but distant from one another at the nucleotide/protein sequence level. The non-synonymous/synonymous substitution (Ka/Ks) ratio analysis suggested a positive evolutionary gene selection for Pi6C and various Pi7C. The selective deletion of the first reaction centre cysteine residues that are structure-level-paired but sequence-level-distant in PI-II illustrates the flexibility of PI-II domains and suggests the functionality of their transient gene versions during evolution.

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“…Only one study was found in the literature that suggested that eye depth could be efficiently selected in two vastly different environments (Johansen et al, 1965); but details were lacking in the abstract, and the full report was never published. Several studies have shown that deep eye depth is dominant to shallow (Li et al, 2005;Mosquera et al, 2009). The correlations involving tuber eye depth among the locations were low to moderate, ranging from 0.12 to 0.30.…”

Section: Ratingmentioning

confidence: 99%

Early Generation Selection within a Diploid Hybrid Solanum tuberosum Groups Phureja and Stenotomum Population for the Intense Yellow-flesh Creamer Potato Market

Haynes¹,

Zotarelli²,

Christensen³

et al. 2019

horts

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Consumer demand for specialty market potatoes has been growing. Cultivated South American diploid potatoes possess great variation for skin and flesh colors, shape, and taste. A long-day adapted population of Solanum tuberosum groups Phureja and Stenotomum (phu-stn) was evaluated for characteristics associated with the type known as papa criolla or papa amarilla in South America. Tubers have intense yellow flesh and may be fried or roasted and eaten whole. A U.S. northern location (Maine), representative of a seed growing region, and two southern locations (Florida and New Mexico), representative of potato growing regions near large Hispanic populations, evaluated yellow-fleshed clones selected within a phu-stn population. Agreement between selectors at two locations was greater than 50%. Tuber skin color and shape were highly correlated between locations; flesh color and tuber dormancy moderately so; eye depth had low correlation between locations; and appearance and skin texture had low or no correlation between locations. Tuber dormancy was generally short, but a few longer dormant clones were identified. There were significant differences among clones for yields, with the highest yields occurring in Maine. More intense evaluations are planned for a subset of these clones before possible release as new varieties. Future breeding efforts will be undertaken to lengthen tuber dormancy in this population.

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Inheritance and genetic mapping of tuber eye depth in cultivated diploid potatoes

Cited by 52 publications

References 19 publications

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

Selective Loss of Cysteine Residues and Disulphide Bonds in a Potato Proteinase Inhibitor II Family

Early Generation Selection within a Diploid Hybrid Solanum tuberosum Groups Phureja and Stenotomum Population for the Intense Yellow-flesh Creamer Potato Market

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