Published on Thu Jul 22 2021

The five Urochola spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

Higgins, J., Tomaszewska, P., Pellny, T. K., Castiblanco, V., Arango, J., Tohme, J., Schwarzacher, T., Mitchell, R., Heslop-Harrison, J. S., De Vega, J. J.

Urochola is a genus of tropical and subtropical grasses widely sown as forage to feed ruminants in the tropics. We explored the genetic make-up and population structure in 111 accessions. These accessions are conserved from wild materials from collection sites at their centre of origin in Africa. We used RNA-seq to generate 1,167,542 stringently selected SNP markers.

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Abstract

Background and Aims: Urochola (syn. Brachiaria, and including some Panicum and Megathyrus) is a genus of tropical and subtropical grasses widely sown as forage to feed ruminants in the tropics. A better understanding of the diversity among Urochola spp. allow us to leverage its varying ploidy levels and genome composition to accelerate its improvement, following the example from other crop genera. Methods: We explored the genetic make-up and population structure in 111 accessions, which comprise the five Urochola species used for the development of commercial cultivars. These accessions are conserved from wild materials from collection sites at their centre of origin in Africa. We used RNA-seq, averaging 40M reads per accession, to generate 1,167,542 stringently selected SNP markers that tentatively encompassed the complete Urochola gene pool used in breeding. Key Results: We identified ten subpopulations, which had no relation with geographical origin and represented ten independent gene pools, and two groups of admixed accessions. Our results support a division in U. decumbens by ploidy, with a diploid subpopulation closely related to U. ruziziensis, and a tetraploid subpopulation closely related to U. brizantha. We observed highly differentiated gene pools in U. brizantha, which were not related with origin or ploidy. Particularly, one U. brizantha subpopulation clustered distant from the other U. brizantha and U. decumbens subpopulations, so likely containing unexplored alleles. We also identified a well-supported subpopulation containing both polyploid U. decumbens and U. brizantha accessions; this was the only group containing more than one species and tentatively constitutes an independent "mixed" gene pool for both species. We observed two gene pools in U. humidicola. One subpopulation, "humidicola-2", was much less common but likely includes the only known sexual accession in the species. Conclusions: Our results offered a definitive picture of the available diversity in Urochola to inform breeding and resolve questions raised by previous studies. It also allowed us identifying prospective founders to enrich the breeding gene pool and to develop genotyping and genotype-phenotype association mapping experiments.