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Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye

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Abstract

Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens).

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  1. Agriculture Research Service, Forage and Range Research Laboratory (FRRL), United States Department of Agriculture, Utah State University, Logan, UT, 84322-6300, USA

    Lan Yun, Steve R. Larson, Ivan W. Mott, Kevin B. Jensen & Jack E. Staub

  2. Inner Mongolia Agriculture University, Hohhot, 010019, China

    Lan Yun

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  1. Lan Yun
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  2. Steve R. Larson
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Correspondence to Steve R. Larson.

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Communicated by S. Hohmann.

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Table S1. List of 213 new perennial wildrye rhizome EST markers derived from rhizome and tiller meristems of creeping × basin wildrye hybrids.

Table S2. Comprehensive list of 107 gene models between 55.21 and 55.95 Mb on Brachypodium Chromosome 3 (Bd3), list of 75 corresponding perennial wildrye rhizome ESTs aligned between 55.21 and 55.95 Mb of Bd3, and an integrated list of 106 discrete gene loci comprised of single or overlapping Brachypodium gene models and perennial wildrye rhizome ESTs.

Figure S1. Images of perennial wildrye species, hybrids, and rhizomes. (A and B) Comparison of spring regrowth in May, 2 years after establishment with 2 m spacing between propagules. (C and D) Comparison of flowering plants in July, two and 3 years after establishment. (E and F) Subterranean tiller and rhizome buds from creeping × basin wildrye hybrids exposed in October. (G) Creeping wildrye rhizomes, including one growing point, exposed about 9 cm below the frozen surface in January.

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Yun, L., Larson, S.R., Mott, I.W. et al. Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye. Mol Genet Genomics 289, 383–397 (2014). https://doi.org/10.1007/s00438-014-0817-5

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