genes G C A T T A C G G C A T Article Genetic Diversity and Population Structure of a Rhodes Grass (Chloris gayana) Collection Alemayehu Teressa Negawo 1 , Meki S. Muktar 1 , Yilikal Assefa 1 , Jean Hanson 1 , Alieu M. Sartie 1,2 , Ermias Habte 1 and Chris S. Jones 1,3, *   Citation: Negawo, A.T.; Muktar, M.S.; Assefa, Y.; Hanson, J.; Sartie, A.M.; Habte, E.; Jones, C.S. Genetic Diversity and Population Structure of a Rhodes Grass (Chloris gayana) Collection. Genes 2021, 12, 1233. https://doi.org/10.3390/ genes12081233 Academic Editor: Marcelo Carena Received: 22 May 2021 Accepted: 5 August 2021 Published: 10 August 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia; A.Teressa@cgiar.org (A.T.N.); M.Shehabu@cgiar.org (M.S.M.); Y.Assefa@cgiar.org (Y.A.); jeanhanson2010@gmail.com (J.H.); sartiealieu@hotmail.com (A.M.S.); e.habte@cgiar.org (E.H.) 2 The Pacific Community (SPC), Private Mail Bag, Suva, Fiji 3 Feed and Forage Development Program, International Livestock Research Institute, Nairobi 00100, Kenya * Correspondence: c.s.jones@cgiar.org Abstract: Rhodes grass (Chloris gayana Kunth) is one of the most important forage grasses used throughout the tropical and subtropical regions of the world. Enhancing the conservation and use of genetic resources requires the development of knowledge and understanding about the existing global diversity of the species. In this study, 104 Rhodes grass accessions, held in trust in the ILRI forage genebank, were characterized using DArTSeq markers to evaluate the genetic diversity and population structure, and to develop representative subsets, of the collection. The genotyping produced 193,988 SNP and 142,522 SilicoDArT markers with an average polymorphic information content of 0.18 and 0.26, respectively. Hierarchical clustering using selected informative markers showed the presence of two and three main clusters using SNP and SilicoDArT markers, respectively, with a cophenetic correction coefficient of 82%. Bayesian population structure analysis also showed the presence of two main subpopulations using both marker types indicating the existence of significant genetic variation in the collection. A representative subset, containing 21 accessions from diverse origins, was developed using the SNP markers. In general, the results revealed substantial genetic diversity in the Rhodes grass collection, and the generated molecular information, together with the developed subset, should help enhance the management, use and improvement of Rhodes grass germplasm in the future. Keywords: DArTSeq markers; genetic diversity; Rhodes grass (Chloris gayana); subset 1. Introduction Rhodes grass (Chloris gayana Kunth) is an important tropical C4 grass widely used throughout the tropical and subtropical regions of the world [1–3]. It is either an annual or perennial, high yielding and good quality forage grass that is also used as a cover crop to improve soil fertility and reduce soil nematodes [1,2]. Rhodes grass is a primarily cross-pollinated diploid or tetraploid (with a basic chro- mosome number, x = 10) highly polymorphic forage grass species [2]. It has a deep root system and can withstand extended periods of drought [1], and grows in a wide range of ecologies and soil types [1,2] with no known economically important biotic stressor [2]. It is reported to be a salt-excluding halophyte that secretes excess salts transported into the leaves [4] and this characteristic makes this grass species one of the most important candidate forages for economic utilization in saline environments such as in saline affected irrigation farming [4–6]. Several cultivars with improved performance, particularly in drought and low temperature prone areas, have been developed and commercialized [2]. A few cultivars have also been reported to be frost tolerant [1,2]. Diploid cultivars have been reported to be more resistant/tolerant to drought, salt, low temperatures, pests and Genes 2021, 12, 1233. https://doi.org/10.3390/genes12081233 https://www.mdpi.com/journal/genes