Insights Into the Genetic Architecture of Complex Traits in Napier Grass (Cenchrus purpureus) and QTL Regions Governing Forage Biomass Yield, Water Use Efficiency and Feed Quality Traits.

Meki S Muktar,Ki-Won Lee,Jiyu Zhang,Yilikal Assefa,Ermias Habte,Abel Teshome,Chris S Jones,Alemayehu T Negawo

doi:10.3389/fpls.2021.678862

Abstract

Napier grass is the most important perennial tropical grass native to Sub-Saharan Africa and widely grown in tropical and subtropical regions around the world, primarily as a forage crop for animal feed, but with potential as an energy crop and in a wide range of other areas. Genomic resources have recently been developed for Napier grass that need to be deployed for genetic improvement and molecular dissection of important agro-morphological and feed quality traits. From a diverse set of Napier grass genotypes assembled from two independent collections, a subset of 84 genotypes (although a small population size, the genotypes were selected to best represent the genetic diversity of the collections) were selected and evaluated for 2 years in dry (DS) and wet (WS) seasons under three soil moisture conditions: moderate water stress in DS (DS-MWS); severe water stress in DS (DS-SWS) and, under rainfed (RF) conditions in WS (WS-RF). Data for agro-morphological and feed quality traits, adjusted for the spatial heterogeneity in the experimental blocks, were collected over a 2-year period from 2018 to 2020. A total of 135,706 molecular markers were filtered, after removing markers with missing values >10% and a minor allele frequency (MAF) <5%, from the high-density genome-wide markers generated previously using the genotyping by sequencing (GBS) method of the DArTseq platform. A genome-wide association study (GWAS), using two different mixed linear model algorithms implemented in the GAPIT R package, identified more than 35 QTL regions and markers associated with agronomic, morphological, and water-use efficiency traits. QTL regions governing purple pigmentation and feed quality traits were also identified. The identified markers will be useful in the genetic improvement of Napier grass through the application of marker-assisted selection and for further characterization and map-based cloning of the QTLs.

Highlights

Improving livestock feeds and forages will play a key role in global food and nutrition security and have the potential to contribute to the strategy of achieving climate-smart agriculture, restoring degraded lands and decreasing greenhouse gas emission intensities (Bryan et al, 2013; Peters et al, 2013; Belay, 2019; Paul et al, 2020)
The phenotypic measurements of the agronomic, morphological, and feed quality traits were collected on a genetically diverse set of 84 Napier grass genotypes evaluated over a 2-year period under three soil moisture conditions in the wet (WS) and dry (DS) seasons
As shown by the spatial trend (Figures 1A,C), plants grown in the middle part of block 4 performed worse compared to the plants in the other blocks which was consistent with visual observations

Summary

Introduction

Improving livestock feeds and forages will play a key role in global food and nutrition security and have the potential to contribute to the strategy of achieving climate-smart agriculture, restoring degraded lands and decreasing greenhouse gas emission intensities (Bryan et al, 2013; Peters et al, 2013; Belay, 2019; Paul et al, 2020). To cope with the shortage of feeds during the dry season, many farmers in subSaharan Africa (SSA) rely mainly on drought-tolerant perennial grasses, such as Napier grass, that can produce a reasonable amount of feed under limited water availability (Lukuyu et al, 2012; Kabirizi et al, 2015). Napier grass is known for its high biomass production (up to 78 tons of dry matter per hectare annually), year-round availability under limited irrigation, ability to withstand repeated cuttings when harvested multiple times, resistance to most pests and diseases, ease of establishment and rapid propagation and, fast regrowth capacity (Anderson et al, 2008; Lukuyu et al, 2012; Kabirizi et al, 2015). Reports have shown the potential of Napier grass for biofuel, bioremediation and paper production (Madakadze et al, 2010; Rengsirikul et al, 2013; Tsai and Tsai, 2016; Rocha-Meneses et al, 2020)

Methods

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Discussion

Conclusion