A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality

Sun, Rui; Chang, Yuansheng; Yang, Fang; Wang, Yi; Li, Hui; Zhao, Yongsheng; Chen, Dongmei; Wu, Ting; Zhang, Xinzhong; Han, Zhenhai

doi:10.1186/s12864-015-1946-x

Cited by 77 publications

(78 citation statements)

References 67 publications

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“…Since the release of the genome sequence of apple 36 and the consequent extensive development of whole genome genotyping SNP arrays, 22,37 several high-density genetic maps of apple were constructed. Most of them are integrated bi-parental maps of one family, where the number of individuals ranges from 118 to 297, comprising different type of markers (for example, SNP+SSR for a total of 1,016 markers; 34 SNP+SSR for a total of 2 579 markers; 28 SNP+SSR for a total of 601 markers; 65 3 441 SNP (ref. 66)) and GBS based linkage maps comprising 3 967 SNP (ref.…”

Section: Discussionmentioning

confidence: 99%

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

et al. 2016

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Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.

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Section: Discussionmentioning

confidence: 99%

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

et al. 2016

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“…Restriction site associated DNA sequencing (RAD-seq) represents a feasible and flexible strategy for population SNP detection in plants (Miller et al, 2007;Du et al, 2012;Sun et al, 2015). Quite simply, the genome's complexity could be reduced by a represented reduced representation library (RRL) that enriched numbers of RAD loci (or restriction enzyme-based specific genomic fragments); in-parallel RRL sequencing of sample DNAs allowed genome-wide SNP detection for researchers.…”

Section: Introductionmentioning

confidence: 99%

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

Shu

Zheng

2016

Dendrobiology

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Compared to angiosperms, conifers represent more complex genomes with larger giga-genome size. To detect large-scale single nucleotide polymorphisms (SNPs), whole genome sequencing of a conifer population is still unaffordable. In this work, we report the use of DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), an ecological and economic important conifer in China. SLAF libraries of 18 parent clones of a Chinese fir 2.5 generation seed orchard were sequenced and a total of 117,924 SLAFs were developed. We detected 147,376 SNPs from these SLAFs; 146,231 of them represented simple nucleotide change in A/G, C/T, A/C, A/T, C/G or G/T. The most frequent SNPs occurred in C/T (34.3%), while the majority of SNPs (68.2%) belonged to transition events (A/G and C/T). Notably, all the sequenced samples had high portion (78.2-80.9%) of common SNPs indicating that the Chinese fir genomes tended to change its nucleotides at common loci. 48,406 informative SNPs were then successfully utilized to genotype the tested samples (n = 18) followed by a phylogenetic tree to clarify their genetic relationship. Furthermore, a set of very high linkage disequilibrium (0.51-1.00) were identified from these informative SNPs. In brief, our work demonstrated that SLAF-seq is an alternative and cost-effectively high-throughput approach for large-scale SNP exploitation in Chinese fir. While the obtained SNPs offer useful marker resource for further genetic and genomic studies and will be helpful for Chinese fir breeding programs.

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“…However, several apple cultivars containing two non‐functional mutant alleles of the Ma1 locus also have lower pH values in fruit, which suggests that the Ma1 gene is not the only genetic determinant of fruit acidity in apple (Ma et al ., ). Moreover, in addition to the Ma1 gene, another major QTL for fruit acidity was identified on LG8 in different segregating populations (Kenis et al ., ; Ma et al ., ; Sun et al ., ). Hence, our knowledge on genetic basis of the biosynthesis and accumulation of malic acid in apple fruit is still limited.…”

Section: Introductionmentioning

confidence: 97%

A Ma10 gene encoding P‐type ATPase is involved in fruit organic acid accumulation in apple

Liao

Fang

et al. 2018

Plant Biotechnology Journal

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Acidity is one of the main determinants of fruit organoleptic quality. Here, comparative transcriptome analysis was conducted between two cultivars that showed a significant difference in fruit acidity, but contained homozygous non-functional alleles at the major gene Ma1 locus controlling apple fruit acidity. A candidate gene for fruit acidity, designated M10, was identified. The M10 gene encodes a P-type proton pump, P -ATPase, which facilitates malate uptake into the vacuole. The Ma10 gene is significantly associated with fruit malate content, accounting for ~7.5% of the observed phenotypic variation in apple germplasm. Subcellular localization assay showed that the Ma10 is targeted to the tonoplast. Overexpression of the Ma10 gene can complement the defect in proton transport of the mutant YAK2 yeast strain and enhance the accumulation of malic acid in apple callus. Moreover, its ectopic expression in tomato induces a decrease in fruit pH. These results suggest that the Ma10 gene has the capacity for proton pumping and plays an important role in fruit vacuolar acidification in apple. Our study provides useful knowledge towards comprehensive understanding of the complex mechanism regulating apple fruit acidity.

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A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality

Cited by 77 publications

References 67 publications

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

A Ma10 gene encoding P‐type ATPase is involved in fruit organic acid accumulation in apple

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