Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections

peer-reviewedNapier grass is an important tropical forage-grass and of growing potential as an energy crop. One-hundred-five Napier grass accessions, encompassing two independent collections, were subjected to genotyping by sequencing which generated a set of high-density genome-wide markers together with short sequence reads. The reads, averaging 54 nucleotides, were mapped to the pearl millet genome and the closest genes and annotation information were used to select candidate genes linked to key forage traits. 980 highly polymorphic SNP markers, distributed across the genome, were used to assess population structure and diversity with seven-subgroups identified. A few representative accessions were selected with the objective of distributing subsets of a manageable size for further evaluation. Genome-wide linkage disequilibrium (LD) analyses revealed a fast LD-decay, on average 2.54 kbp, in the combined population with a slower LD-decay in the ILRI collection compared with the EMBRAPA collection, the significance of which is discussed. This initiative generated high-density markers with a good distribution across the genome. The diversity analysis revealed the existence of a substantial amount of variation in the ILRI collection and identified some unique materials from the EMBRAPA collection, demonstrating the potential of the overall population for further genetic and marker-trait-association studies

Opportunities for Napier Grass (Pennisetum purpureum) Improvement Using Molecular Genetics

Napier grass (Pennisetum purpureum Schumach.) is a fast-growing perennial grass native to Sub-Saharan Africa that is widely grown across the tropical and subtropical regions of the world. It is a multipurpose forage crop, primarily used to feed cattle in cut and carry feeding systems. Characterization and diversity studies on a small collection of Napier grasses have identified a moderate level of genetic variation and highlighted the availability of some good agronomic traits, particularly high biomass production, as a forage crop. However, very little information exists on precise phenotyping, genotyping and the application of molecular technologies to Napier grass improvement using modern genomic tools which have been applied in advancing the selection and breeding of important food crops. In this review paper, existing information on genetic resources, molecular diversity, yield and nutritional quality of Napier grass will be discussed. Recent findings on characterizing disease resistance and abiotic stress (drought) tolerance will also be highlighted. Finally, opportunities and future prospects for better conservation and use arising from the application of modern genomic tools in Napier grass phenotyping and genotyping will be discussed

Exploring the variation in grain and straw yield and straw quality traits of improved varieties of Tef [Eragrostis tef (Zucc.) Trotter]

Tef [Eragrostis tef (Zucc.) Trotter] is an indigenous Ethiopian cereal providing healthy and nutritious diets for people and a palatable straw for livestock. Thirty-five released varieties and a local check were grown at two locations over two years in Ethiopia to investigate the variation in grain and straw yield and straw quality traits of tef. The investigated traits were grain yield (GY), straw yield (STY), crude protein (CP), in vitro organic matter digestibility (IVOMD), metabolizable energy (ME), acid detergent fiber (ADF), neutral detergent fiber (NDF) and acid detergent lignin (ADL). GY, CP, IVOMD and ME were significantly (P < 0.01) affected by the variety of tef, the cultivation environment and their interactions. The performances of the GY, CP, IVOMD and ME traits were higher (P < 0.01) at mid-altitude, in Debre Zeit, compared to the high-altitude site, Holetta, and in 2016 than 2015. Similarly, the associations observed between GY and STY, among CP, ME and IVOMD, and among NDF, ADF and ADL were significant (P<0.01) and positive. Conversely, the association between yield and quality traits was significant and negative. The present study also identified four groups of varieties based on their grain and straw yield and straw quality traits, with some varieties performing above the mean for both yield and quality traits. Hence, varieties like Melko which possess better grain and straw yield and quality traits could be promoted for immediate utilization as a dual-purpose variety or as a parental line in changing the existing tef breeding strategy that focuses on grain yield improvement alone

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

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

Productivity and feed quality performance of Napier grass (Cenchrus purpureus) genotypes growing under different soil moisture levels

In the semi-arid and arid environments of Sub-Sharan Africa, forage availability throughout the year is insufficient and highly limited during the dry seasons due to limited precipitation. Thus, the identification of drought stress-tolerant forage cultivars is one of the main activities in forage development programs. In this study, Napier grass (Cenchrus purpureus), an important forage crop in Eastern and Central Africa that is broadly adapted to produce across tropical environments, was evaluated for its water use efficiency and production performance under field drought stress conditions. Eighty-four Napier grass genotypes were evaluated for their drought stress tolerance from 2018 to 2020 using agro-morphological and feed quality traits under two soil moisture stress regimes during the dry season, i.e., moderate (MWS) and severe (SWS) water stress conditions, and under rainfed conditions in the wet season (wet). Overall, the results indicated the existence of genotype variation for the traits studied. In general, the growth and productivity of the genotypes declined under SWS compared to MWS conditions. High biomass-yielding genotypes with enhanced WUE were consistently observed across harvests in each soil moisture stress regime. In addition, the top biomass-yielding genotypes produced the highest annual crude protein yield, indicating the possibility of developing high-feed-quality Napier grass genotypes for drought stress environments

Analysis of global Napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections

Abstract Genetic diversity amongst genotypes of several Napier grass collections was analyzed and compared with the diversity in a set of open pollinated progeny plants. A total of 114,881 SNP and 46,293 SilicoDArT genome-wide markers were generated on 574 Napier grass genotypes. Of these, 86% of the SNP and 66% of the SilicoDArT markers were mapped onto the fourteen chromosomes of the Napier grass genome. For genetic diversity analysis, a subset of highly polymorphic and informative SNP markers was filtered using genomic position information, a maximum of 10% missing values, a minimum minor allele frequency of 5%, and a maximum linkage-disequilibrium value of 0.5. Extensive genetic variation, with an average Nei’s genetic distance value of 0.23, was identified in the material. The genotypes clustered into three major and eleven sub-clusters with high levels of genetic variation contained both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among the collections and that some overlap and redundancy occurred between collections. The progeny plants were genetically diverse and divergent from the germplasm collections, with an average F ST value of 0.08. We also reported QTL regions associated with forage biomass yield based on field phenotype data measured on a subset of the Napier grass collections. The findings of this study offer useful information for Napier grass breeding strategies, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections

Molecular markers as a tool for germplasm acquisition to enhance the genetic diversity of a Napier grass (<i>Cenchrus purpureus</i> syn. <i>Pennisetum purpureum</i>) collection

At the International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia, 171 germplasm accessions of Napier grass were studied using 20 SSR markers with the objective of assessing the allelic richness and genetic diversity of the collections held at ILRI and the Brazilian Agricultural Research Corporation (EMBRAPA), and to determine distinct accessions to be introduced to enhance the diversity in each of the genebank collections. A total of 148 alleles were observed in the whole collection, of which 140 and 93 alleles were observed in the ILRI and EMBRAPA collections, respectively. Fifty-five and 8 alleles were found to be unique to the ILRI and EMBRAPA collections, respectively, while 85 alleles were shared between the collections. The number of alleles per marker ranged from 1 to 23 with an average value of 7.4 across both collections. The heterozygosity per locus ranged from 0.000 to 0.808 with an average value of 0.463. A principal coordinate analysis grouped accessions into 3 main groups, whereas a hierarchical cluster analysis indicated 4 main clusters. From a genebank management and conservation perspective, the marker profile of the accessions was used in the process of selecting and acquiring distinct lines to be added to the ILRI and EMBRAPA collections. Accordingly, 54 accessions and elite lines were selected and introduced from EMBRAPA to the ILRI collection, while 8 distinct accessions from ILRI were added to the EMBRAPA collection. In general, a useful marker profile of an expanded Napier grass collection has been generated which could be used to enhance the conservation, use and management of the available genetic resources of this important forage crop