Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum

Malleswari Gelli, Sharon E. Mitchell, Kan Liu, Thomas E. Clemente, Donald P. Weeks, Chi Zhang, David R. Holding, Ismail M. Dweikat

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Background: Sorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization. Results: A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha-1 fertilizer) and low N (0 kg.ha-1 fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8 %. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions. Conclusions: Co-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.

Original languageEnglish (US)
Article number16
JournalBMC plant biology
Volume16
Issue number1
DOIs
StatePublished - Jan 13 2016

Fingerprint

agronomic traits
quantitative trait loci
nitrogen
chromosomes
genes
nitrogen fertilizers
sequence analysis
fertilizers
hormone metabolism
ferredoxins
seed storage proteins
nitrogen metabolism
glycolysis
nitrate reductase
phenotypic variation
marker-assisted selection
plant hormones
inbred lines
genotyping
single nucleotide polymorphism

Keywords

  • Agronomic traits
  • Differentially expressed gene transcripts
  • Genotyping-by-sequencing
  • Illumina RNA-seq
  • Nitrogen fertilizer
  • QTL mapping
  • Sorghum

ASJC Scopus subject areas

  • Plant Science

Cite this

Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. / Gelli, Malleswari; Mitchell, Sharon E.; Liu, Kan; Clemente, Thomas E.; Weeks, Donald P.; Zhang, Chi; Holding, David R.; Dweikat, Ismail M.

In: BMC plant biology, Vol. 16, No. 1, 16, 13.01.2016.

Research output: Contribution to journalArticle

Gelli, Malleswari ; Mitchell, Sharon E. ; Liu, Kan ; Clemente, Thomas E. ; Weeks, Donald P. ; Zhang, Chi ; Holding, David R. ; Dweikat, Ismail M. / Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. In: BMC plant biology. 2016 ; Vol. 16, No. 1.
@article{2326bbb688a24be2a09e6f713c8ce65a,
title = "Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum",
abstract = "Background: Sorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization. Results: A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha-1 fertilizer) and low N (0 kg.ha-1 fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8 {\%}. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions. Conclusions: Co-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.",
keywords = "Agronomic traits, Differentially expressed gene transcripts, Genotyping-by-sequencing, Illumina RNA-seq, Nitrogen fertilizer, QTL mapping, Sorghum",
author = "Malleswari Gelli and Mitchell, {Sharon E.} and Kan Liu and Clemente, {Thomas E.} and Weeks, {Donald P.} and Chi Zhang and Holding, {David R.} and Dweikat, {Ismail M.}",
year = "2016",
month = "1",
day = "13",
doi = "10.1186/s12870-015-0696-x",
language = "English (US)",
volume = "16",
journal = "BMC Plant Biology",
issn = "1471-2229",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum

AU - Gelli, Malleswari

AU - Mitchell, Sharon E.

AU - Liu, Kan

AU - Clemente, Thomas E.

AU - Weeks, Donald P.

AU - Zhang, Chi

AU - Holding, David R.

AU - Dweikat, Ismail M.

PY - 2016/1/13

Y1 - 2016/1/13

N2 - Background: Sorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization. Results: A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha-1 fertilizer) and low N (0 kg.ha-1 fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8 %. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions. Conclusions: Co-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.

AB - Background: Sorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization. Results: A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha-1 fertilizer) and low N (0 kg.ha-1 fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8 %. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions. Conclusions: Co-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.

KW - Agronomic traits

KW - Differentially expressed gene transcripts

KW - Genotyping-by-sequencing

KW - Illumina RNA-seq

KW - Nitrogen fertilizer

KW - QTL mapping

KW - Sorghum

UR - http://www.scopus.com/inward/record.url?scp=84953776281&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84953776281&partnerID=8YFLogxK

U2 - 10.1186/s12870-015-0696-x

DO - 10.1186/s12870-015-0696-x

M3 - Article

C2 - 26759170

AN - SCOPUS:84953776281

VL - 16

JO - BMC Plant Biology

JF - BMC Plant Biology

SN - 1471-2229

IS - 1

M1 - 16

ER -