The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development

Abstract

Background Sweetpotato ( Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. Results Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1 ) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11 , sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. Conclusions We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development. Electronic supplementary material The online version of this article (10.1186/s12870-019-1708-z) contains supplementary material, which is available to authorized users.

Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato

“…Advances in discovering the molecular mechanisms of important agronomic traits for this outcrossing crop are highly limited because of its complicated genetic and genomic characteristics. Due to the importance of sweet potato to humans and the development of sequencing technologies, more resources have been generated in recent years, such as the haplotype-resolved genome of I. batatas 4 , wild genomes of the ancestors Ipomoea triloba and Ipomoea trifida 5,6 , resequencing and transcriptome datasets for cultivated sweet potato 5,7 . Utilizing these genomic resources, many genes that are associated with storage root development and nutrient accumulation have been identified 5,7,8 .…”

“…Utilizing these genomic resources, many genes that are associated with storage root development and nutrient accumulation have been identified 5,7,8 . In addition, linkage or association analysis has also identified several loci or candidate genes that are responsible for storage root-related traits 6,[9][10][11] . However, our insights into the processes and genetic regulatory networks in the storage roots of sweet potato remain limited.…”

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

“…Such investigations may pave the way into exploiting these regulators for breeding purposes. A recent study carried out in the sweet potato wild ancestor Ipomoea trifida, highlighted how investigations on WRKY gene family in wild relatives can boost the molecular breeding of cultivated species 13 . However, our knowledge is still not complete and therefore WRKY gene biodiversity remains unlocked in many species.…”

Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops

“…In recent years many large‐scale efforts have sought to further understand these crops using genome sequences (Xu et al , ; D'Hont et al , ; Wang et al , ; Tamiru et al , ; Yang et al , ; Li et al , ) and genome diversity studies (Bredeson et al , ; Hardigan et al , ; Nyine et al , ; Christelová et al , ; Muñoz‐Rodríguez et al , ; Němečková et al , ), genetic selection (Wolfe et al , ), molecular markers (QTLs) (Monden and Tahara, ; Kim et al , ; Sharma and Bryan, ), and comparative transcriptome resources (Kundapura Venkataramana et al , ; Sarah et al , ; van Wesemael et al , ; Cenci et al , ) widely developed alongside morphologic, agronomic and phenotypic classifications (Oliveira et al , ; Rahajeng and Rahayuningsih, ; Dépigny et al , ; Girma et al , ; van Wesemael et al , ). The progress of the CGIAR Research Program on Roots, Tubers and Bananas (http://www.rtb.cgiar.org), applying genomics‐assisted breeding to RTBs, has recently been reviewed (Friedmann et al , ).…”