Orthologous comparisons of the Hd1 region across genera reveal hd1 gene lability within diploid oryza species and disruptions to microsynteny in sorghum

Abhijit Sanyal, Jetty S S Ammiraju, Fei Lu, Yeisoo Yu, Teri Rambo, Jennifer Currie, Kristi Kollura, Hye Ran Kim, Jinfeng Chen, Jianxin Ma, Phillip San Miguel, Chen Mingsheng, Rod A Wing, Scott A. Jackson

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice. Consistent with other observations at the adh1/adh2, monoculm1, and sh2/a1 loci in grass species, we found high gene colinearity in the Hd1 region amidst size differences that were lineage specific and long terminal repeat retrotransposon driven. Unexpectedly, the Hd1 gene was deleted in O. glaberrima, whereas the O. rufipogon and O. punctata copies had degenerative mutations, suggesting that other heading date loci might compensate for the loss or nonfunctionality of Hd1 in these species. Compared with the japonica Hd1 region, the orthologous region in sorghum exhibited micro-rearrangements including gene translocations, seven additional genes, and a gene triplication and truncation event predating the divergence from Oryza.

Original languageEnglish (US)
Pages (from-to)2487-2506
Number of pages20
JournalMolecular Biology and Evolution
Volume27
Issue number11
DOIs
StatePublished - Nov 2010

Fingerprint

Sorghum
Oryza
sorghum
Diploidy
Sorghum (Poaceae)
diploidy
gene
heading
Genes
rice
genes
domestication
loci
Retroelements
terminal repeat sequences
Terminal Repeat Sequences
Gene Rearrangement
retrotransposons
Poaceae
quantitative traits

Keywords

  • comparative genomics
  • genome evolution
  • microsynteny
  • transposons

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Orthologous comparisons of the Hd1 region across genera reveal hd1 gene lability within diploid oryza species and disruptions to microsynteny in sorghum. / Sanyal, Abhijit; Ammiraju, Jetty S S; Lu, Fei; Yu, Yeisoo; Rambo, Teri; Currie, Jennifer; Kollura, Kristi; Kim, Hye Ran; Chen, Jinfeng; Ma, Jianxin; San Miguel, Phillip; Mingsheng, Chen; Wing, Rod A; Jackson, Scott A.

In: Molecular Biology and Evolution, Vol. 27, No. 11, 11.2010, p. 2487-2506.

Research output: Contribution to journalArticle

Sanyal, A, Ammiraju, JSS, Lu, F, Yu, Y, Rambo, T, Currie, J, Kollura, K, Kim, HR, Chen, J, Ma, J, San Miguel, P, Mingsheng, C, Wing, RA & Jackson, SA 2010, 'Orthologous comparisons of the Hd1 region across genera reveal hd1 gene lability within diploid oryza species and disruptions to microsynteny in sorghum', Molecular Biology and Evolution, vol. 27, no. 11, pp. 2487-2506. https://doi.org/10.1093/molbev/msq133
Sanyal, Abhijit ; Ammiraju, Jetty S S ; Lu, Fei ; Yu, Yeisoo ; Rambo, Teri ; Currie, Jennifer ; Kollura, Kristi ; Kim, Hye Ran ; Chen, Jinfeng ; Ma, Jianxin ; San Miguel, Phillip ; Mingsheng, Chen ; Wing, Rod A ; Jackson, Scott A. / Orthologous comparisons of the Hd1 region across genera reveal hd1 gene lability within diploid oryza species and disruptions to microsynteny in sorghum. In: Molecular Biology and Evolution. 2010 ; Vol. 27, No. 11. pp. 2487-2506.
@article{79693be41ca94ba18bf4640c2be5778a,
title = "Orthologous comparisons of the Hd1 region across genera reveal hd1 gene lability within diploid oryza species and disruptions to microsynteny in sorghum",
abstract = "Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice. Consistent with other observations at the adh1/adh2, monoculm1, and sh2/a1 loci in grass species, we found high gene colinearity in the Hd1 region amidst size differences that were lineage specific and long terminal repeat retrotransposon driven. Unexpectedly, the Hd1 gene was deleted in O. glaberrima, whereas the O. rufipogon and O. punctata copies had degenerative mutations, suggesting that other heading date loci might compensate for the loss or nonfunctionality of Hd1 in these species. Compared with the japonica Hd1 region, the orthologous region in sorghum exhibited micro-rearrangements including gene translocations, seven additional genes, and a gene triplication and truncation event predating the divergence from Oryza.",
keywords = "comparative genomics, genome evolution, microsynteny, transposons",
author = "Abhijit Sanyal and Ammiraju, {Jetty S S} and Fei Lu and Yeisoo Yu and Teri Rambo and Jennifer Currie and Kristi Kollura and Kim, {Hye Ran} and Jinfeng Chen and Jianxin Ma and {San Miguel}, Phillip and Chen Mingsheng and Wing, {Rod A} and Jackson, {Scott A.}",
year = "2010",
month = "11",
doi = "10.1093/molbev/msq133",
language = "English (US)",
volume = "27",
pages = "2487--2506",
journal = "Molecular Biology and Evolution",
issn = "0737-4038",
publisher = "Oxford University Press",
number = "11",

}

TY - JOUR

T1 - Orthologous comparisons of the Hd1 region across genera reveal hd1 gene lability within diploid oryza species and disruptions to microsynteny in sorghum

AU - Sanyal, Abhijit

AU - Ammiraju, Jetty S S

AU - Lu, Fei

AU - Yu, Yeisoo

AU - Rambo, Teri

AU - Currie, Jennifer

AU - Kollura, Kristi

AU - Kim, Hye Ran

AU - Chen, Jinfeng

AU - Ma, Jianxin

AU - San Miguel, Phillip

AU - Mingsheng, Chen

AU - Wing, Rod A

AU - Jackson, Scott A.

PY - 2010/11

Y1 - 2010/11

N2 - Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice. Consistent with other observations at the adh1/adh2, monoculm1, and sh2/a1 loci in grass species, we found high gene colinearity in the Hd1 region amidst size differences that were lineage specific and long terminal repeat retrotransposon driven. Unexpectedly, the Hd1 gene was deleted in O. glaberrima, whereas the O. rufipogon and O. punctata copies had degenerative mutations, suggesting that other heading date loci might compensate for the loss or nonfunctionality of Hd1 in these species. Compared with the japonica Hd1 region, the orthologous region in sorghum exhibited micro-rearrangements including gene translocations, seven additional genes, and a gene triplication and truncation event predating the divergence from Oryza.

AB - Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice. Consistent with other observations at the adh1/adh2, monoculm1, and sh2/a1 loci in grass species, we found high gene colinearity in the Hd1 region amidst size differences that were lineage specific and long terminal repeat retrotransposon driven. Unexpectedly, the Hd1 gene was deleted in O. glaberrima, whereas the O. rufipogon and O. punctata copies had degenerative mutations, suggesting that other heading date loci might compensate for the loss or nonfunctionality of Hd1 in these species. Compared with the japonica Hd1 region, the orthologous region in sorghum exhibited micro-rearrangements including gene translocations, seven additional genes, and a gene triplication and truncation event predating the divergence from Oryza.

KW - comparative genomics

KW - genome evolution

KW - microsynteny

KW - transposons

UR - http://www.scopus.com/inward/record.url?scp=77958134353&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77958134353&partnerID=8YFLogxK

U2 - 10.1093/molbev/msq133

DO - 10.1093/molbev/msq133

M3 - Article

VL - 27

SP - 2487

EP - 2506

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

SN - 0737-4038

IS - 11

ER -