Novel genes and alleles of the BTB/POZ protein family in Oryza rufipogon

• Published in: Scientific reports Vol. 13; no. 1; p. 15466
• Main Authors: Mandal, Swarupa Nanda, Sanchez, Jacobo, Bhowmick, Rakesh, Bello, Oluwatobi R., Van-Beek, Coenraad R., de los Reyes, Benildo G.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19-09-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208; 631/449; Alleles; Cultivars; Cultivation; Evolutionary genetics; Gene duplication; Gene pool; Genes; Genomes; Grain cultivation; Humanities and Social Sciences; Hybridization; multidisciplinary; Oryza rufipogon; Oryza sativa japonica; Phylogeny; Regulatory sequences; Science; Science (multidisciplinary); Sequence analysis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-41269-0

The BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (
OsBTB
) have been identified in cultivated rice (
Oryza sativa
), their conservation, novelty, and potential applications for allele mining in
O. rufipogon
, the direct progenitor of
O. sativa
ssp.
japonica
and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (
OrBTB
) across the genome of
O. rufipogon
as outcomes of tandem duplication events. Phylogenetic grouping of duplicated
OrBTB
genes was supported by the analysis of gene sequences and protein domain architecture, shedding some light on their evolution and functional divergence. The
O. rufipogon
genome encodes nine novel BTB/POZ genes with orthologs in its distant cousins in the family Poaceae (
Sorghum bicolor
,
Brachypodium distachyon
), but such orthologs appeared to have been lost in its domesticated descendant,
O. sativa
ssp.
japonica
. Comparative sequence analysis and structure comparisons of novel
OrBTB
genes revealed that diverged upstream regulatory sequences and regulon restructuring are the key features of the evolution of this large gene family. Novel genes from the wild progenitor serve as a reservoir of potential new alleles that can bring novel functions to cultivars when introgressed by wide hybridization. This study establishes a foundation for hypothesis-driven functional genomic studies and their applications for widening the genetic base of rice cultivars through the introgression of novel genes or alleles from the exotic gene pool.