A High-Density Genetic Map of an Allohexaploid Brassica Doubled Haploid Population Reveals Quantitative Trait Loci for Pollen Viability and Fertility

Su Yang, Sheng Chen, Kangni Zhang, Lan Li, Yuling Yin, Rafaqat A. Gill, Guijun Yan, Jinling Meng, Wallace A. Cowling, Weijun Zhou

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Abstract

A doubled haploid (DH) mapping population was obtained from microspore culture of an allohexaploid F-1 from the cross between two recently-synthesized allohexaploid Brassica lines. We used single nucleotide polymorphism (SNP) genetic variation based on restriction-site associated DNA (RAD) sequencing to construct a high density genetic linkage map of the population. RAD libraries were constructed from the genomic DNA of both parents and 146 DH progenies. A total of 2.87G reads with an average sequencing depth of 2.59 x were obtained in the parents and of 1.41 x in the progeny. A total of 290,422 SNPs were identified from clustering of RAD reads, from which we developed 7,950 high quality SNP markers that segregated normally (1:1) in the population. The linkage map contained all 27 chromosomes from the parental A, B and C genomes with a total genetic distance of 5725.19 cM and an average of 0.75 cM between adjacent markers. Genetic distance on non-integrated linkage groups was 1534.23 cM, or 21% of total genetic distance. Out of 146 DH progenies, 91 had a complete set of 27 chromosomes as expected of a hexaploid species, and 21 out of 27 chromosomes showed high collinearity between the physical and linkage maps. The loss of chromosome(s) or chromosome segment(s) in the DH population was associated with a reduction in pollen viability. Twenty-five additive QTL were associated with pollen viability and fertility-related traits (seed number, seed yield, pod length, plant height, 1000-seed weight). In addition, 44 intra-genomic and 18 inter-genomic epistatic QTL pairs were detected for 4 phenotypic traits. This provides confidence that the DH population may be selected for improved pollen viability and fertility in a future allohexaploid Brassica species.

Original languageEnglish
Article number1161
Number of pages18
JournalFrontiers in Plant Science
Volume9
DOIs
Publication statusPublished - 28 Aug 2018

Cite this

@article{5afb8a7c073743bd809822e59358e8b5,
title = "A High-Density Genetic Map of an Allohexaploid Brassica Doubled Haploid Population Reveals Quantitative Trait Loci for Pollen Viability and Fertility",
abstract = "A doubled haploid (DH) mapping population was obtained from microspore culture of an allohexaploid F-1 from the cross between two recently-synthesized allohexaploid Brassica lines. We used single nucleotide polymorphism (SNP) genetic variation based on restriction-site associated DNA (RAD) sequencing to construct a high density genetic linkage map of the population. RAD libraries were constructed from the genomic DNA of both parents and 146 DH progenies. A total of 2.87G reads with an average sequencing depth of 2.59 x were obtained in the parents and of 1.41 x in the progeny. A total of 290,422 SNPs were identified from clustering of RAD reads, from which we developed 7,950 high quality SNP markers that segregated normally (1:1) in the population. The linkage map contained all 27 chromosomes from the parental A, B and C genomes with a total genetic distance of 5725.19 cM and an average of 0.75 cM between adjacent markers. Genetic distance on non-integrated linkage groups was 1534.23 cM, or 21{\%} of total genetic distance. Out of 146 DH progenies, 91 had a complete set of 27 chromosomes as expected of a hexaploid species, and 21 out of 27 chromosomes showed high collinearity between the physical and linkage maps. The loss of chromosome(s) or chromosome segment(s) in the DH population was associated with a reduction in pollen viability. Twenty-five additive QTL were associated with pollen viability and fertility-related traits (seed number, seed yield, pod length, plant height, 1000-seed weight). In addition, 44 intra-genomic and 18 inter-genomic epistatic QTL pairs were detected for 4 phenotypic traits. This provides confidence that the DH population may be selected for improved pollen viability and fertility in a future allohexaploid Brassica species.",
keywords = "restriction-site associated DNA sequencing, allohexaploid Brassica, single nucleotide polymorphism, loss of chromosomes, collinearity, QTL mapping, GENOME, DISCOVERY, SEQUENCE, MARKERS, JUNCEA, YIELD, NAPUS, QTL",
author = "Su Yang and Sheng Chen and Kangni Zhang and Lan Li and Yuling Yin and Gill, {Rafaqat A.} and Guijun Yan and Jinling Meng and Cowling, {Wallace A.} and Weijun Zhou",
year = "2018",
month = "8",
day = "28",
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language = "English",
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A High-Density Genetic Map of an Allohexaploid Brassica Doubled Haploid Population Reveals Quantitative Trait Loci for Pollen Viability and Fertility. / Yang, Su; Chen, Sheng; Zhang, Kangni; Li, Lan; Yin, Yuling; Gill, Rafaqat A.; Yan, Guijun; Meng, Jinling; Cowling, Wallace A.; Zhou, Weijun.

In: Frontiers in Plant Science, Vol. 9, 1161, 28.08.2018.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A High-Density Genetic Map of an Allohexaploid Brassica Doubled Haploid Population Reveals Quantitative Trait Loci for Pollen Viability and Fertility

AU - Yang, Su

AU - Chen, Sheng

AU - Zhang, Kangni

AU - Li, Lan

AU - Yin, Yuling

AU - Gill, Rafaqat A.

AU - Yan, Guijun

AU - Meng, Jinling

AU - Cowling, Wallace A.

AU - Zhou, Weijun

PY - 2018/8/28

Y1 - 2018/8/28

N2 - A doubled haploid (DH) mapping population was obtained from microspore culture of an allohexaploid F-1 from the cross between two recently-synthesized allohexaploid Brassica lines. We used single nucleotide polymorphism (SNP) genetic variation based on restriction-site associated DNA (RAD) sequencing to construct a high density genetic linkage map of the population. RAD libraries were constructed from the genomic DNA of both parents and 146 DH progenies. A total of 2.87G reads with an average sequencing depth of 2.59 x were obtained in the parents and of 1.41 x in the progeny. A total of 290,422 SNPs were identified from clustering of RAD reads, from which we developed 7,950 high quality SNP markers that segregated normally (1:1) in the population. The linkage map contained all 27 chromosomes from the parental A, B and C genomes with a total genetic distance of 5725.19 cM and an average of 0.75 cM between adjacent markers. Genetic distance on non-integrated linkage groups was 1534.23 cM, or 21% of total genetic distance. Out of 146 DH progenies, 91 had a complete set of 27 chromosomes as expected of a hexaploid species, and 21 out of 27 chromosomes showed high collinearity between the physical and linkage maps. The loss of chromosome(s) or chromosome segment(s) in the DH population was associated with a reduction in pollen viability. Twenty-five additive QTL were associated with pollen viability and fertility-related traits (seed number, seed yield, pod length, plant height, 1000-seed weight). In addition, 44 intra-genomic and 18 inter-genomic epistatic QTL pairs were detected for 4 phenotypic traits. This provides confidence that the DH population may be selected for improved pollen viability and fertility in a future allohexaploid Brassica species.

AB - A doubled haploid (DH) mapping population was obtained from microspore culture of an allohexaploid F-1 from the cross between two recently-synthesized allohexaploid Brassica lines. We used single nucleotide polymorphism (SNP) genetic variation based on restriction-site associated DNA (RAD) sequencing to construct a high density genetic linkage map of the population. RAD libraries were constructed from the genomic DNA of both parents and 146 DH progenies. A total of 2.87G reads with an average sequencing depth of 2.59 x were obtained in the parents and of 1.41 x in the progeny. A total of 290,422 SNPs were identified from clustering of RAD reads, from which we developed 7,950 high quality SNP markers that segregated normally (1:1) in the population. The linkage map contained all 27 chromosomes from the parental A, B and C genomes with a total genetic distance of 5725.19 cM and an average of 0.75 cM between adjacent markers. Genetic distance on non-integrated linkage groups was 1534.23 cM, or 21% of total genetic distance. Out of 146 DH progenies, 91 had a complete set of 27 chromosomes as expected of a hexaploid species, and 21 out of 27 chromosomes showed high collinearity between the physical and linkage maps. The loss of chromosome(s) or chromosome segment(s) in the DH population was associated with a reduction in pollen viability. Twenty-five additive QTL were associated with pollen viability and fertility-related traits (seed number, seed yield, pod length, plant height, 1000-seed weight). In addition, 44 intra-genomic and 18 inter-genomic epistatic QTL pairs were detected for 4 phenotypic traits. This provides confidence that the DH population may be selected for improved pollen viability and fertility in a future allohexaploid Brassica species.

KW - restriction-site associated DNA sequencing

KW - allohexaploid Brassica

KW - single nucleotide polymorphism

KW - loss of chromosomes

KW - collinearity

KW - QTL mapping

KW - GENOME

KW - DISCOVERY

KW - SEQUENCE

KW - MARKERS

KW - JUNCEA

KW - YIELD

KW - NAPUS

KW - QTL

U2 - 10.3389/fpls.2018.01161

DO - 10.3389/fpls.2018.01161

M3 - Article

VL - 9

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 1161

ER -