Genetic Diversity and Population Structure of a Rhodes Grass (Chloris gayana) Collection.

Alemayehu Teressa Negawo,Alieu M Sartie,Ermias Habte,Meki S Muktar,Chris S Jones,Yilikal Assefa,Jean Hanson

doi:10.3390/genes12081233

Alemayehu Teressa Negawo, Alieu M Sartie + Show 5 more

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https://doi.org/10.3390/genes12081233

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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.

Highlights

Rhodes grass (Chloris gayana Kunth) is an important tropical C4 grass widely used throughout the tropical and subtropical regions of the world [1,2,3]
After filtering the data with missing percentage (≤20%) and polymorphic information content (PIC) (≥0.2), 30,279 and 59,164 SNP and SilicoDArT markers, respectively, were retained for preliminary analysis to select the top 1000 markers contributing to genetic differentiation among the accessions
The results revealed the presence of a broad range of diversity in the collection, as demonstrated by the hierarchical clustering as well as Bayesian population structure analysis

Summary

Introduction

Rhodes grass (Chloris gayana Kunth) is an important tropical C4 grass widely used throughout the tropical and subtropical regions of the world [1,2,3] It is either an annual or perennial, high yielding and good quality forage grass that is 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 chromosome 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]. Rhodes grass has some good agronomic and morphological characteristics that make it a resilient forage crop to consider under the current dynamics of climate change to increase the availability of feed resources for sustainable livestock production

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