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White Guinea Yam Genome Sequence Offers Insight Into Dioecy Plants

NEW YORK (GenomeWeb) – An international team of researchers has sequenced the genome of the white Guinea yam, a staple food crop in Africa.

Yams encompass the members of the Dioscorea genus, which covers some 450 species, though the most popular species in West and Central Africa is D. rotundata, or the white Guinea yam. However, members of the Dioscorea genus like D. rotundata have separate male and female plants, called trait called dioecy, which can hamper cultivation.

Researchers led by Ryohei Terauchi at the Iwate Biotechnology Institute Research Center in Japan have analyzed the D. rotundata genome to bolster genomics-associated breeding. As they reported this week in BMC Biology, the researchers generated a 594-megabase reference genome for D. rotundata and homed in on regions that appeared to influence sex determination.

"Having a reference sequence for the white Guinea yam gives us the unique opportunity to gain a better understanding of dioecy, a very rare trait in flowering plants," author Benjamen White from the Earlham Institute said in a statement. "Understanding this trait and having a genomic resource for white Guinea yam will be invaluable in breeding a better yam, one that will improve food security in West and Central Africa, and the livelihood of smallholder farmers there."

The authors collected DNA from leaves of an individual D. rotundata plant from an open-pollination breeding line for sequencing. Using a combination of paired-end, mate-pair, and BAC-end sequencing, they generated 85.14 gigabases of reads, which gave them about 149.4X coverage of the D. rotundata genome.

With the ALLPATHS-LG assembler and the SSPACE scaffolding software, they generated more than 4,723 scaffolds with a genome size of 594 megabases, slightly larger than what had been estimated by k-mer and flow cytometry analyses.

By drawing on genetic data from progeny of a cross of two heterozygous D. rotundata breeding lines, the researchers pieced together a linkage map. They anchored the scaffolds to the map to yield 21 linkage groups or chromosome-scale pseudo-molecules.

Using RNA-seq data from various D. rotundata tissues, the researchers predicted that the yam genome contains 26,198 genes. Some 5,557 of these genes were orthologous to ones found in Brachypodium distachyon, Oryza sativa, and Arabidopsis thaliana, but 12,625 others appeared to have no orthologs or paralogs in those species. Of the genes without homologs, almost a third were expressed in tuber tissue from D. rotundata, a tissue type the other species lack.

Additionally, a phylogenetic analysis based on the 2,381 orthologous protein-coding genes placed D. rotundata apart from the other monocotyledon plants. This suggested to the researchers that D. rotundata diversified independently of those plants.

The authors also scoured the D. rotundata for the region that determined whether the plant was male or female. They conducted a QTL-seq analysis of 253 individual plants that were male, female, non-flowering, or were monoecious, that is, both male and female, to find a region of pseudo-chromosome 11 that was homozygous in the male plants, but heterozygous in the female plants.

While the researchers noted that the ZZ phenotype stably produced male plants, they found that the ZW phenotype was less stable. Though it generally led to female plants, it sometimes also resulted in monoecious or male plants, they said.

Monoecious plants, they said, could be a boon for yam farming as self-pollination of such lines could be developed into inbred lines housed desired traits.

"[The genome] will help to overcome some of the many challenges facing yam farmers in Africa and other parts of the world," Terauchi added in a statement.