QTL for tuber morphology traits in diploid potato

Hara-Skrzypiec, Agnieszka; Śliwka, Jadwiga; Jakuczun, H.; Zimnoch‐Guzowska, E.

doi:10.1007/s13353-018-0433-x

Cited by 27 publications

(66 citation statements)

References 24 publications

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“…Previously published markers were mainly developed with diploid potato [19,20,21,22]. but not directly on the tetraploid level.…”

Section: Discussionmentioning

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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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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“…Previously published markers were mainly developed with diploid potato [19,20,21,22]. but not directly on the tetraploid level.…”

Section: Discussionmentioning

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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“…Alternate population structures, such as testcross populations, have also been realized by utilizing crosses between heterozygous material and inbred wild potato species-which contain alleles for self-compatibility-or a synthetic doubled monoploid (DM) that suffers from severe inbreeding depression (Hosaka and Hanneman 1998;Felcher et al 2012;Manrique-Carpintero et al 2015). Several diploid potato populations have demonstrated the utility of genome reduction for identifying QTL for yield and other tuber traits (Lindqvist-Kreuze et al 2015;Manrique-Carpintero et al 2015Hara-Skrzypiec et al 2018). However, genotyping uncertainties and coarse genetic maps hampered past efforts to clearly define discrete genomic intervals underlying important agronomic traits.…”

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confidence: 99%

Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato

et al. 2019

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Marand et al. use a high-resolution recombination map to dissect the genetic components of yield in diploid potato. Regions of recalcitrant heterozygosity in the inbred parent co-localized with elevated recombination rates, signatures of selection, and tissue-specific gene expression... 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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“…Tetraploid potato has a complex genetics, and molecular marker development is difficult. Previously developed markers were mainly based on diploid (Bakker et al 2004; Asano et al 2012; Zhu et al 2015; Hara-Skrzypiec et al 2018), but markers developed directly at the tetraploid level were rarely reported. This study based on the maturity-related genetic segments mined on chromosome 5, a total of 52 pairs of specific primers were designed and synthesized, and eight molecular markers were developed with a development efficiency of 15.4%.…”

Section: Discussionmentioning

confidence: 99%

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

Jin

et al. 2018

Preprint

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16Maturity is one of the important traits of potato. In order to get the genetic segment of potato early maturity trait, 17 a tetraploid potato maturity segregation population of Zhongshu 19 × Zhongshu 3 was used for genetic analysis 18 through the combination of high throughput simplified genome sequencing (2b-RAD) and bulked segregation 19 analysis (BSA). A genetic segment related to the early maturity trait at the 3.7~4.2 Mb locus on the short arm of 20 chromosome 5 was obtained and eight markers were developed based on this segment, while five of them were 21 closely linked to the early maturity trait loci. Moreover, 42 SSR markers were developed based on the reference 22 sequence of DM. Finally, a genetic map of chromosome 5 contained 50 markers was constructed using the 23 Tetraploidmap software. The total map length was 172 cM with an average genetic distance of 3.44 cM. 24Combining with phenotypic data of the segregation population, we mapped the early maturity trait QTL with the 25 contribution of 33.55% on the short arm of chromosome 5, located at 84cM between the flanking markers 26 SSR5-85-1 and SCAR5-8 with the physical interval of 471kb. Gene annotation showed that there exist 34 genes 27 in this region, 12 of them are unknown function. Among the other 22 annotated genes, E3 ubiquitin ligase gene 28 PUB14 may be related to maturity and regulate tuber formation. Our fine mapping of the early maturity QTL 29 made a solid foundation for cloning of the early maturity controlled gene or genes. 30 Key words：potato ·genetic segment · early maturity trait · marker development · QTL mapping 31Author contribution statement 33 GL and LJ conceived the project, provided idea and designed the whole experiments; XL and JZ conceived the 34 project and performed the molecular marker development and analysis; JX contributed to the maturity 35 phenotyping of the mapping population; SD performed the parents crossing of the mapping population; CB and 36 JH performed the field management of potato materials. All authors read and approved the final manuscript. 37 Key message 38Early maturity site was mapped using a tetraploid potato segregation population derived from cv. Zhongshu 19 39 and Zhongshu 3. One major QTL with 33.55% contribution to early maturity was fine mapped in physical 40 interval of 471kb on chromosome 5. potato (2n = 4x = 48) is highly heterozygous, with high frequency of genetic recombination and 87 severe recession after self-fertilization (Manrique-Carpintero et al. 2018). The molecular marker is difficult to 88 develop. The diploid potato chromosome number is small, the genetic background is relatively simple, and it is 89 easy to carry out genetic analysis and operation. Therefore, the development of potato markers and genetic map 90 construction is mainly at the diploid level, and is done mainly with the use of the traditional QTL mapping 91 analysis method, whereas fewer studies are conducted on tetraploid materials. Although most of the studies have 92 mapped QTLs on chromosome 5, there are no m...

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QTL for tuber morphology traits in diploid potato

Cited by 27 publications

References 24 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.)

Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato

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

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