Evolution of PHAS loci in the young spike of Allohexaploid wheat

BMC Genomics
Rongzhi ZhangGenying Li

Abstract

PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, which include two categories, 21-nt (nucleotide) and 24-nt phasiRNAs. They are triggered by miR2118 and miR2275 respectively, in premeiotic and meiotic anthers of rice, maize and other grass species. Wheat (Triticum aestivum) with three closely related subgenomes (subA, subB and subD), is a model of allopolyploid in plants. Knowledge about the role of phasiRNAs in the inflorescence development of wheat is absent until now, and the evolution of PHAS loci in polyploid plants is also unavailable. Using 261 small RNA expression datasets from various tissues, a batch of PHAS (phasiRNA precursors) loci were identified in the young spike of wheat, most of which were regulated by miR2118 and miR2275 in their target site regions. Dissection of PHAS and their trigger miRNAs among the diploid (AA and DD), tetraploid (AABB) and hexaploid (AABBDD) genomes of Triticum indicated that distribution of PHAS loci were dominant randomly in local chromosomes, while miR2118 was dominant only in the subB genome. The diversity of PHAS loci in the...Continue Reading

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Citations

Mar 20, 2021·Frontiers in Plant Science·Neeti Sanan-MishraSunil K Mukherjee
May 11, 2021·Frontiers in Molecular Biosciences·Jiali YuMargaret E Staton
Oct 22, 2021·Frontiers in Plant Science·Arun S SeetharamMatthew B Hufford

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Datasets Mentioned

BETA
SRR3690680
SRR3680677
SRR3680678
SRR3680679
SRR5464508
SRR5464518
SRR5464520
SRR5464524
SRR5460939
SRR5460949

Methods Mentioned

BETA
RNA-seq
transgenic

Software Mentioned

Cleaveland
DEseq
Targetfinder
ShortStack
RSEM
Pheatmap
R
Shortstack package
R package
Trimmomatic

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