A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations

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A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations. / Jiang, Ning; Zhang, Fengjun; Wu, Jinhua; Chen, Yue; Hu, Xiaohua; Fang, Ou; Leach, Lindsey J.; Wang, Di; Luo, Zewei.

In: Theoretical and Applied Genetics, Vol. 129, No. 9, 09.2016, p. 1739–1757.

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Jiang, Ning ; Zhang, Fengjun ; Wu, Jinhua ; Chen, Yue ; Hu, Xiaohua ; Fang, Ou ; Leach, Lindsey J. ; Wang, Di ; Luo, Zewei. / A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations. In: Theoretical and Applied Genetics. 2016 ; Vol. 129, No. 9. pp. 1739–1757.

Bibtex

@article{0a7ceddc958040c59cf3fb79aad5a589,
title = "A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations",
abstract = "Advent of the next generation sequencing techniques motivates recent interest in developing sequence-based identification and genotyping of genome-wide genetic variants in large populations, with RAD-seq being a typical example. Without taking proper account for the fact that chloroplast and rRNA genes may occupy up to 60 % of the resulting sequence reads, the current RAD-seq design could be very inefficient for plant and crop species. We presented here a generic computational tool to optimize RAD-seq design in any plant species and experimentally tested the optimized design by implementing it to screen for and genotype sequence variants in four plant populations of diploid and autotetraploid Arabidopsis and potato Solanum tuberosum. Sequence data from the optimized RAD-seq experiments shows that the undesirable chloroplast and rRNA contributed sequence reads can be controlled at 3–10 %. Additionally, the optimized RAD-seq method enables pre-design of the required uniformity and density in coverage of the high quality sequence polymorphic markers over the genome of interest and genotyping of large plant or crop populations at a competitive cost in comparison to other mainstream rivals in the literature.",
author = "Ning Jiang and Fengjun Zhang and Jinhua Wu and Yue Chen and Xiaohua Hu and Ou Fang and Leach, {Lindsey J.} and Di Wang and Zewei Luo",
year = "2016",
month = sep,
doi = "10.1007/s00122-016-2736-9",
language = "English",
volume = "129",
pages = "1739–1757",
journal = "Theoretical and Applied Genetics",
issn = "0040-5752",
publisher = "Springer",
number = "9",

}

RIS

TY - JOUR

T1 - A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations

AU - Jiang, Ning

AU - Zhang, Fengjun

AU - Wu, Jinhua

AU - Chen, Yue

AU - Hu, Xiaohua

AU - Fang, Ou

AU - Leach, Lindsey J.

AU - Wang, Di

AU - Luo, Zewei

PY - 2016/9

Y1 - 2016/9

N2 - Advent of the next generation sequencing techniques motivates recent interest in developing sequence-based identification and genotyping of genome-wide genetic variants in large populations, with RAD-seq being a typical example. Without taking proper account for the fact that chloroplast and rRNA genes may occupy up to 60 % of the resulting sequence reads, the current RAD-seq design could be very inefficient for plant and crop species. We presented here a generic computational tool to optimize RAD-seq design in any plant species and experimentally tested the optimized design by implementing it to screen for and genotype sequence variants in four plant populations of diploid and autotetraploid Arabidopsis and potato Solanum tuberosum. Sequence data from the optimized RAD-seq experiments shows that the undesirable chloroplast and rRNA contributed sequence reads can be controlled at 3–10 %. Additionally, the optimized RAD-seq method enables pre-design of the required uniformity and density in coverage of the high quality sequence polymorphic markers over the genome of interest and genotyping of large plant or crop populations at a competitive cost in comparison to other mainstream rivals in the literature.

AB - Advent of the next generation sequencing techniques motivates recent interest in developing sequence-based identification and genotyping of genome-wide genetic variants in large populations, with RAD-seq being a typical example. Without taking proper account for the fact that chloroplast and rRNA genes may occupy up to 60 % of the resulting sequence reads, the current RAD-seq design could be very inefficient for plant and crop species. We presented here a generic computational tool to optimize RAD-seq design in any plant species and experimentally tested the optimized design by implementing it to screen for and genotype sequence variants in four plant populations of diploid and autotetraploid Arabidopsis and potato Solanum tuberosum. Sequence data from the optimized RAD-seq experiments shows that the undesirable chloroplast and rRNA contributed sequence reads can be controlled at 3–10 %. Additionally, the optimized RAD-seq method enables pre-design of the required uniformity and density in coverage of the high quality sequence polymorphic markers over the genome of interest and genotyping of large plant or crop populations at a competitive cost in comparison to other mainstream rivals in the literature.

U2 - 10.1007/s00122-016-2736-9

DO - 10.1007/s00122-016-2736-9

M3 - Article

VL - 129

SP - 1739

EP - 1757

JO - Theoretical and Applied Genetics

JF - Theoretical and Applied Genetics

SN - 0040-5752

IS - 9

ER -