Copy number variation ofTdDofcontrols solid-stemmed architecture in wheat

Stem solidness is an important agronomic trait of durum (Triticum turgidumL. var.durum) and bread (Triticum aestivumL.) wheat that provides resistance to the wheat stem sawfly. This dominant trait is conferred by theSSt1locus on chromosome 3B. However, the molecular identity and mechanisms underpinning stem solidness have not been identified. Here, we demonstrate that copy number variation ofTdDof, a gene encoding a putative DNA binding with one finger protein, controls the stem solidness trait in wheat. Using map-based cloning, we localizedTdDofto within a physical interval of 2.1 Mb inside theSSt1locus. Molecular analysis revealed that hollow-stemmed wheat cultivars such as Kronos carry a single copy ofTdDof, whereas solid-stemmed cultivars such as CDC Fortitude carry multiple identical copies of the gene. Deletion of allTdDofcopies from CDC Fortitude resulted in the loss of stem solidness, whereas the transgenic overexpression ofTdDofrestored stem solidness in theTdDofdeletion mutantpithless1and conferred stem solidness in Kronos. In solid-stemmed cultivars, increasedTdDofexpression was correlated with the down-regulation of genes whose orthologs have been implicated in programmed cell death (PCD) in other species. Anatomical and histochemical analyses revealed that hollow-stemmed lines had stronger PCD-associated signals in the pith cells compared to solid-stemmed lines, which suggests copy number-dependent expression ofTdDofcould be directly or indirectly involved in the negative regulation of PCD. These findings provide opportunities to manipulate stem development in wheat and other monocots for agricultural or industrial purposes.

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Extreme copy number variation at a tRNA ligase affecting phenology and fitness in yellow monkeyflowers

10.1101/392183 ◽

2018 ◽

Author(s):

Thom Nelson ◽

Patrick Monnahan ◽

Mariah McIntosh ◽

Findley R. Finseth ◽

Kayli Anderson ◽

...

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Molecular Mechanisms ◽

Wild Population ◽

Intermediate Frequency ◽

Single Copy ◽

Multiple Traits ◽

Fluctuating Selection ◽

Mendelian Segregation ◽

Number Variation

AbstractCopy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (Migut.N02091; RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate frequency three-copy variants of RLG1a (trip+; 5/35 = 14%), and trip+ lines exhibited elevated RLG1a expression under multiple conditions. trip+ carriers, in addition to being over-represented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (P < 0.05). In wild population samples, we discovered an additional rare RLG1a variant (high+) that carries 250-300 copies of RLG1a totaling ∼5.7Mb (20-40% of a chromosome). In the progeny of a high+ carrier, Mendelian segregation of diagnostic alleles and qPCR-based copy counts indicate that high+ is a single tandem array unlinked from the single copy RLG1a locus. In the wild, high+ carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; both p < 0.01), while single copy individuals were twice as fecund as either CNV type in a lush year (2016: p < 0.005). Our results demonstrate fluctuating selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.

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