A tandem segmental duplication (TSD) in green revolution gene Rht‐D1b region underlies plant height variation

Abstract

Summary• Rht-D1c (Rht10) carried by Chinese wheat (Triticum aestivum) line Aibian 1 is an allele at the Rht-D1 locus. Among the Rht-1 alleles, little is known about Rht-D1c although it determines an extreme dwarf phenotype in wheat.• Here, we cloned and functionally characterized Rht-D1c using a combination of Southern blotting, target region sequencing, gene expression analysis and transgenic experiments.• We found that the Rht-D1c allele was generated through a tandem segmental duplication (TSD) of a > 1 Mb region, resulting in two copies of the Rht-D1b. Two copies of Rht-D1b in the TSD were three-fold more effective in reducing plant height than a single copy, and transformation with a segment containing the tandemly duplicated copy of Rht-D1b resulted in the same level of reduction of plant height as the original copy in Aibian 1.• Our results suggest that changes in gene copy number are one of the important sources of genetic diversity and some of these changes could be directly associated with important traits in crops.

Genome Structures and Transcriptomes Signify Niche Adaptation for the Multiple-Ion-Tolerant Extremophyte Schrenkiella parvula

“…Structural variation can lead to CNV of genes, which, in turn, affects gene dosage and transcription strength (Stranger et al, 2007;Schlattl et al, 2011;Massouras et al, 2012;Haraksingh and Snyder, 2013). In plants, many examples exist for the copy number of a gene or genome segment associated with phenotype changes (Cook et al, 2012;Li et al, 2012;Maron et al, 2013;Nitcher et al, 2013), and genome-wide CNVs appear to predict phenotypes to some extent Muñoz-Amatriaín et al, 2013). The S. parvula genome is characterized by a higher copy number of genes associated with transporter activity (Dassanayake et al, 2011a).…”

A System for Dosage-Based Functional Genomics in Poplar

“…For example, in animals, copy number variation has major effects on developmental traits and disease (Henrichsen et al, 2009;Craddock et al, 2010;Stankiewicz and Lupski, 2010;Alvarez and Akey, 2012). In plants, copy number variation has been identified in multiple species and demonstrated to affect important agronomic traits (Horiguchi et al, 2009;Pearce et al, 2011;Cook et al, 2012;Díaz et al, 2012;Li et al, 2012;Wingen et al, 2012;Ma et al, 2013). On a wider scale, when lesions encompass a larger chromosomal region or even an entire chromosome, gene dosage effects are responsible for aneuploidy syndromes.…”

Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species

“…For example, the deletion of the Ms2 region ( X25 - Xsdauw30 , Supplementary Data 7) in the synthetic wheat SW7 impeded further mapping of MS2 within the Xsdauw20 – Xsdauw32 interval. The RMs2 linkage has a tandem segmental duplication over a 1 Mb region28, which apparently was responsible for our exceptionally low recombination in the Ms2 region among the RMs2 -based populations (popE and popF, Supplementary Fig. 4).…”