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Title: UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study

Abstract

Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative fraction of the genome has become feasible for any crop. Nevertheless, most genotyping-by-sequencing (GBS) methods are geared towards obtaining large numbers of markers at low sequence depth, which excludes their application in heterozygous individuals. However, bioinformatics pipelines often lack the flexibility to deal with paired-end reads or to be applied in polyploid species.

Authors:
 [1];  [2];  [3];  [4];  [1];  [1];  [5];  [1]; ORCiD logo [1]
  1. Univ. of Georgia, Athens, GA (United States)
  2. Univ. of Georgia, Athens, GA (United States); ICRISAT-Nairobi, Nairobi (Kenya); Institute of Plant Breeding, Tifton, GA (United States)
  3. Univ. of Georgia, Athens, GA (United States); ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata (India)
  4. Univ. of Georgia, Athens, GA (United States); North Dakota State Univ., Fargo, ND (United States)
  5. Maseno Univ., Maseno (Kenya)
Publication Date:
Research Org.:
Univ. of Georgia, Athens, GA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1504909
Grant/Contract Number:  
SC0010743
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
BMC Plant Biology
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2229
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Chromosomal rearrangements; Eleusine coracana; E. indica; Finger millet; Genetic mapping; Genotyping-by-sequencing (GBS); GBS-pipeline; Paired-end reads; Polyploid; SNP calling

Citation Formats

Qi, Peng, Gimode, Davis, Saha, Dipnarayan, Schröder, Stephan, Chakraborty, Debkanta, Wang, Xuewen, Dida, Mathews M., Malmberg, Russell L., and Devos, Katrien M. UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study. United States: N. p., 2018. Web. doi:10.1186/s12870-018-1316-3.
Qi, Peng, Gimode, Davis, Saha, Dipnarayan, Schröder, Stephan, Chakraborty, Debkanta, Wang, Xuewen, Dida, Mathews M., Malmberg, Russell L., & Devos, Katrien M. UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study. United States. doi:10.1186/s12870-018-1316-3.
Qi, Peng, Gimode, Davis, Saha, Dipnarayan, Schröder, Stephan, Chakraborty, Debkanta, Wang, Xuewen, Dida, Mathews M., Malmberg, Russell L., and Devos, Katrien M. Fri . "UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study". United States. doi:10.1186/s12870-018-1316-3. https://www.osti.gov/servlets/purl/1504909.
@article{osti_1504909,
title = {UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study},
author = {Qi, Peng and Gimode, Davis and Saha, Dipnarayan and Schröder, Stephan and Chakraborty, Debkanta and Wang, Xuewen and Dida, Mathews M. and Malmberg, Russell L. and Devos, Katrien M.},
abstractNote = {Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative fraction of the genome has become feasible for any crop. Nevertheless, most genotyping-by-sequencing (GBS) methods are geared towards obtaining large numbers of markers at low sequence depth, which excludes their application in heterozygous individuals. However, bioinformatics pipelines often lack the flexibility to deal with paired-end reads or to be applied in polyploid species.},
doi = {10.1186/s12870-018-1316-3},
journal = {BMC Plant Biology},
issn = {1471-2229},
number = 1,
volume = 18,
place = {United States},
year = {2018},
month = {6}
}

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Works referenced in this record:

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011