Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

Abstract

BackgroundRoot and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop.ResultsTo accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage.ConclusionsGuinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0419-x) contains supplementary material, which is available to authorized users.

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 , ).…”

Development of a cost‐effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections

“…Polymorphic SNP flanking sequences (60 bp upstream and 60 bp downstream around the variant position) were selected using SNiPlay3 (Dereeper et al, 2011). In order to assess their putative physical positions, these sequences were then blasted to the D. rotundata reference genome (TDr96_F1 Pseudo_Chromosome: BDMI01000001-BDMI01000021; Tamiru et al, 2017). The physical position of each SNP was defined using their flanking sequences best hit using a BLAST E-value threshold of 1e−30 (Basic Local Alignment Search Tool).…”

“…In our D. alata validation panel, three ploidy levels (2x, 3x and 4x) coexisted (Appendix B). Thus, the KASPar assay could theoretically produce a maximum of seven types of fluorescence signal (Table 1) corresponding to two types of fluorescence signal in homozygous states (2:0 = 3:0 = 4:0; 0:2 = 0:3 = 0:4), the fluorescence signal of mixed and balanced allelic dosages (1:1 for diploids or 2:2 for tetraploids) and the four types of fluorescence signal corresponding to the different possible unbalanced allelic dosages at heterozygotic loci ("polyploid-like" in Table 1) of triploids and tetraploids (1:3; 1:2; 2:1; F I G U R E 1 Location of KASPar SNPs on the D. rotundata reference genome (Tamiru et al, 2017). The 21 linkage group are aligned from left to right.…”

“…Regarding the recent release of yam (Dioscorea spp.) genomic resources (Saski, Bhattacharjee, Scheffler, & Asiedu, 2015;Tamiru et al, 2017), the design of such markers for D. alata collection management would be worthwhile. Indeed, once developed they do not require any specific bioinformatics or wet chemistry skills.…”

Can Parentage Analysis Facilitate Breeding Activities in Root and Tuber Crops?

“…In root and tuber crops, microsatellites have been utilized to determine the progeny-paternity relationship (Table 1). Microsatellites have been used for parentage analysis in yams [32][33][34][35][36][37][38][39], potatoes [44][45][46][48][49][50]52,53,55], cassava [63][64][65][66][67][68][69][70][71][72][73] and sweet potato [76][77][78][79][80][81][82]84,85].…”