Comparative genomic analysis of 5M(g) chromosome of Aegilops geniculata and 5U(u) chromosome of Aegilops umbellulata reveal genic diversity in the tertiary gene pool

Authors: YADAV, INDEJIT YADAV - University Of Maryland; CHUNEJJA, PARVEEN - Punjab Agricultural University; URAY, CHRISTOBAL - John Innes Center; Lazo, Gerard; Gu, Yong; DOLEZEL, JAROSLAV - Institute Of Experimental Biology; RAWAT, NIDHI - University Of Maryland; TIWARI, VIJAY - University Of Maryland

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/22/2023
Publication Date: 7/13/2023
Citation: Yadav, I., Chunejja, P., Uray, C., Lazo, G.R., Gu, Y.Q., Dolezel, J., Rawat, N., Tiwari, V. 2023. Comparative genomic analysis of 5M(g) chromosome of Aegilops geniculata and 5U(u) chromosome of Aegilops umbellulata reveal genic diversity in the tertiary gene pool. Frontiers in Plant Science. 14.Article 1144000. https://doi.org/10.3389/fpls.2023.1144000.
DOI: https://doi.org/10.3389/fpls.2023.1144000

Interpretive Summary: Wheat is one of the most important cereal crops for the global food security. Due to its narrow genetic base, modern bread wheat cultivars face challenges from several abiotic and biotic stresses. Since genetic improvement is the most sustainable approach, finding novel genes and alleles is required to enhance wheat’s genetic diversity. Wheat’s tertiary gene pool is considered gold mine for genetic diversity as novel genes and alleles can be identified and transferred in wheat cultivars. Our findings highlight the diversity of transcription factors and resistance genes, resulting from the differential expansion of the gene families. Both the chromosomes were enriched with the “response to stimulus” category of genes. Phylogenetic study positioned the M genome closer to the D genome, with higher proximity to the A genome than the B genome. Over 4000 genes were impacted by SNPs on 5D, with 4-5% of those genes displaying non-disruptive variations that affect gene function.

Technical Abstract: Aegilops geniculata and Ae. umbellulata are the key members of wheat’s tertiary gene pool and harbor important genes against abiotic and biotic stresses. Homoeologous-group five chromosome (5Uu and 5Mg) has been extensively studied from Ae. geniculata and Ae. umbellulata as they harbor several important genes including Lr57, Lr76, Yr40, Yr70, Sr53 and chromosomal pairing loci. In this study, using chromosome sequencing and RNAseq datasets, we performed comparative studies of 5M, 5U and group 5 wheat chromosomes to study homoeologous genes. Our findings highlight the diversity of transcription factors and resistance genes, resulting from the differential expansion of the gene families. Both the chromosomes were enriched with the “response to stimulus” category of genes. Phylogenetic study positioned the M genome closer to the D genome, with higher proximity to the A genome than the B genome. Over 4000 genes were impacted by SNPs on 5D, with 4-5% of those genes displaying non-disruptive variations that affect gene function.