De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

Abstract

Background Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

MDSi: Multi-omics Database for Setaria italica

“…Foxtail millet is being developed as a novel C 4 model which demands the high-throughput multi-omics data. At present, there were 5 de novo assembled genomic data of 4 elite cultivars [ 8 – 10 , 12 ] and a mutant xiaomi with shorter life cycle [ 11 ]. We also published the RNA-seq data of 11 tissues of xiaomi at different stages [ 11 ].…”

“…A model crop system requires support of sufficient multi-omics data, such as genomics, RNA-seq and metabolic data. At present, the genome of four foxtail millet elite varieties or mutant, including Yugu1 [ 8 ], Zhanggu [ 9 ], TT8 [ 10 ], xiaomi [ 11 ] and Huagu11 [ 12 ] were assembled individually. The genome data of Yugu1 can be accessed in Phytozome [ 13 ], the data of Zhanggu was uploaded in BGI Foxtail millet Database ( http://foxtailmillet.genomics.org.cn ) whereas the information of Huagu11 was stored in China National GeneBank DataBase (CNGBdb) ( https://db.cngb.org/search/project/CNP0000993/ ).…”

The role of phenomics and genomics in delineating the genetic basis of complex traits in millets

“…The study of an organism's entire set of genes or genome aids in finding key genes responsible for critical agronomic, nutritional, and other relevant aspects in millets. The availability of genome assembly in sorghum (McCormick et al 2017), pearl millet (Salson et al 2023), finger millet (Hatakeyama et al 2017;Devos et al 2023), and foxtail millet (Wang et al 2021) is a valuable resource for millets genomic resources. Furthermore, the availability of thousands of genetic stocks of whole genome sequences is the primary genomic resource used to generate additional genomic information, such as the development of molecular markers and the identification of QTLs for target traits, which aids genomics-assisted breeding and genomic selection (Varshney et al 2005(Varshney et al , 2016.…”

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

“…Here, Ser-626-Aln substitution was identified in acetohydroxy acid synthase gene to confer imazethapyr tolerance in Hugua 1. The intraspecies comparison revealed 969,596 SNPs and 156,282 indels with four chromosomal inversions ( Wang et al, 2021c ). The comprehensiveness and accurateness of genome sequence assemblies depend greatly on the techniques used for the task.…”