Sugimoto, K. | Search bioRxiv

bioRxiv2018

Unleashing floret fertility by a mutated homeobox gene improved grain yield during wheat evolution under domestication

Floret fertility is a key trait to determine the number of grains per inflorescence in cereals. During wheat (Triticum sp.) evolution, floret fertility has been increased and current bread wheat (T. aestivum L.) produces three to five grains per spikelet; however, little is known about the genetic basis controlling floret fertility. Here we identify the quantitative trait locus Grain Number Increase 1 (GNI1), encoding a homeodomain leucine zipper class I (HD-Zip I) transcription factor. GNI1 evolved in the Triticeae through gene duplication and functionalization. GNI1 was predominantly expressed in the most apical floret primordia and parts of the rachilla, suggesting that GNI1 inhibits rachilla growth and development. GNI1 expression decreased during wheat evolution, and as a consequence, more fertile florets and grains per spikelet are being produced. Genetic analysis revealed that the reduced-function allele of GNI1-A contributes to increase the number of fertile florets per spikelet. The knockdown of GNI1 in transgenic hexaploid wheat improved fertile floret and grain number. Furthermore, wheat plants carrying the impaired allele increased grain yield under field conditions. Our findings illuminate that gene duplication and functionalization generated evolutionary novelty for floret fertility (i.e. reducing floral numbers) while the mutations towards increased grain production were under selection during wheat evolution under domestication.\n\nSignificance StatementGrain number is a fundamental trait for cereal grain yield; but its underlying genetic basis is mainly unknown in wheat. Here we show for the first time a direct link between increased floret fertility, higher grain number per spike and higher plot-yields of wheat in the field. We have identified GNI1 gene encoding an HD-Zip I transcription factor responsible for increased floret fertility. The wild type allele imposes an inhibitory role specifically during rachilla development, indicating that expression of this protein actively shuts-down grain yield potential; whereas, the reduced-function allele enables more florets and grains to be produced. GNI1 evolved through gene duplication in Triticeae and its mutations were under parallel human selection during wheat and barley evolution under domestication.

plant biology↗

bioRxiv2017

Regulatory Divergence In Wound-Responsive Gene Expression In Domesticated And Wild Tomato

BackgroundThe evolution of cis- and trans-regulatory components of transcription is central to how stress response and tolerance differ across species. However, it remains largely unknown how divergence in TF binding specificity and cis-regulatory sites contribute to the divergence of stress-responsive gene expression between wild and domesticated species.\n\nResultsUsing tomato as model, we analyzed the transcriptional profile of wound-responsive genes in wild Solanum pennellii and domesticated S. lycopersicum. We found that extensive expression divergence of wound-responsive genes is associated with speciation. To assess the degree of trans-regulatory divergence between these two species, 342 and 267 putative cis-regulatory elements (pCREs) in S. lycopersicum and S. pennellii, respectively, were identified that were predictive of wound-induced gene expression. We found that 35-66% of pCREs were conserved across species, suggesting that the remaining proportion (34-65%) of pCREs are species specific. This finding indicates a substantially higher degree of trans-regulatory divergence between these two plant species, which diverged [~]3-7 million years ago, compared to that observed in mouse and human, which diverged [~]100 million years ago. In addition, differences in pCRE sites were significantly associated with differences in wound-responsive gene expression between wild and domesticated tomato orthologs, suggesting the presence of substantial cis-regulatory divergence.\n\nConclusionsOur study provides new insights into the mechanistic basis of how the transcriptional response to wounding is regulated and, importantly, the contribution of cis- and trans-regulatory components to variation in wound-responsive gene expression during species domestication.

evolutionary biology↗