The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth

Abstract

Elephant grass (2n = 4x = 28; Cenchrus purpureus Schumach.), also known as Napier grass, is an important forage grass and potential energy crop in tropical and subtropical regions of Asia, Africa and America. However, no study has yet reported a genome assembly for elephant grass at the chromosome scale. Here, we report a high‐quality chromosome‐scale genome of elephant grass with a total size of 1.97 Gb and a 1.5% heterozygosity rate, obtained using short‐read sequencing, single‐molecule long‐read sequencing and Hi‐C chromosome conformation capture. Evolutionary analysis showed that subgenome A' of elephant grass and pearl millet may have originated from a common ancestor more than 3.22 million years ago (MYA). Further, allotetraploid formation occurred at approximately 6.61 MYA. Syntenic analyses within elephant grass and with other grass species indicated that elephant grass has experienced chromosomal rearrangements. We found that some key enzyme‐encoding gene families related to the biosynthesis of anthocyanidins and flavonoids were expanded and highly expressed in leaves, which probably drives the production of these major anthocyanidin compounds and explains why this elephant grass cultivar has a high anthocyanidin content. In addition, we found a high copy number and transcript levels of genes involved in C4 photosynthesis and hormone signal transduction pathways that may contribute to the fast growth of elephant grass. The availability of elephant grass genome data advances our knowledge of the genetic evolution of elephant grass and will contribute to further biological research and breeding as well as for other polyploid plants in the genus Cenchrus.

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

“…Most of the markers associated with the traits that positively affect feed nutritional quality were from the Napier grass A' genome, while the markers associated with the traits linked with fibre and lignin components were mainly from the B genome, which might indicate a functional differentiation between the two sub-genomes as suggested previously (Yan et al, 2021;Zhang et al, 2020). However, QTL regions overlapping for the positive and negative traits were detected at the bottom of A02 and top of B04.…”

“…The imputation was run on one assembled chromosome (AC) at a time as the run time of the software could not accommodate taking the entire genome at once. The short sequence reads corresponding to the markers were aligned to the recently reported Napier grass genome (Yan et al, 2021) using the bwa mem sequence aligner (Li and Durbin, 2009) and the marker density and distribution across the fourteen ACs of the Napier grass genome was visualized using the synbreed R-package (Wimmer et al, 2012). The sequences were annotated using the genomic information resources of Cenchrus americanus and Setaria italica in the GenBank NCBI blastx tool (https://blast.ncbi.nlm.nih.gov/Blast.cgi) as described previously (Muktar et al, 2019).…”

“…Twelve SNP markers were also in the heterozygous form (for the allele associated with purple colour) in six of the purple genotypes, however, they were in the homozygous form in one purple genotype (CNPGL_92-133-3). The markers were in very strong LD representing large haplotype blocks on B01 and A03 ( Figure 5B), which were the two ACs with high synteny potentially representing the B and A' genomes of Napier grass (Yan et al, 2021).…”

“…Two QTL regions towards the bottom of B01 and the top of A03 were associated with purple pigmentation in Napier grass. The two genomic regions show a high synteny block (Yan et al, 2021) representing the B and A' homeologous chromosomes of Napier grass (dos Reis et al, 2014). Out of the different expanded genes involved in anthocyanin biosynthesis in Napier grass, phenylalanine ammonia lyase (PAL) and chalcone synthase (CHS) were detected on B01 (Yan et al, 2021).…”

“…The generation of high-density genome-wide markers also permitted the construction of the first high-density genetic map of Napier grass (Paudel et al, 2018). The most important breakthrough was the recent reports of the first high-quality chromosome scale genome sequences of Napier grass (Yan et al, 2021; Zhang et al, 2020), in which a 1.97 to 2.07 Gb genome was assembled. This chromosome scale genome sequence offers significant opportunities for the dissection of the genetic architectures of complex traits and the development of improved Napier grass varieties.…”