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

ABSTRACT: BACKGROUND:Root 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. RESULTS:To 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. CONCLUSIONS:Guinea 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.

SUBMITTER: Tamiru M

PROVIDER: S-EPMC5604175 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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

Tamiru Muluneh M Natsume Satoshi S Takagi Hiroki H White Benjamen B Yaegashi Hiroki H Shimizu Motoki M Yoshida Kentaro K Uemura Aiko A Oikawa Kaori K Abe Akira A Urasaki Naoya N Matsumura Hideo H Babil Pachakkil P Yamanaka Shinsuke S Matsumoto Ryo R Muranaka Satoru S Girma Gezahegn G Lopez-Montes Antonio A Gedil Melaku M Bhattacharjee Ranjana R Abberton Michael M Kumar P Lava PL Rabbi Ismail I Tsujimura Mai M Terachi Toru T Haerty Wilfried W Corpas Manuel M Kamoun Sophien S Kahl Günter G Takagi Hiroko H Asiedu Robert R Terauchi Ryohei R

BMC biology 20170919 1

<h4>Background</h4>Root 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. How ...[more]

PMID: 28927400

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Project description:Yam (Dioscorea spp.) is a major food security crop for millions of resource-poor farmers, particularly in West Africa. Soil mineral deficiency is the main challenge in yam production, especially with the dwindling of fallow lands for the indigenous nutrient supply. Cultivars tolerant to available low soil nutrients and responsive to added nutrient supply are viable components of an integrated soil fertility management strategy for sustainable and productive yam farming systems in West Africa. This study's objective was to identify white Guinea yam (D. rotundata) genotypes adapted to available low soil nutrients and responsive to externally added nutrient supply. Twenty advanced breeding lines and a local variety (Amula) were evaluated under contrasting soil fertility, low to expose the crop to available low soil nutrient supply and high to assess the crop response to added mineral fertilizer (NPK) input at Ibadan, Nigeria. The genotypes expressed differential yield response to low soil fertility (LF) stress and added fertilizer input. Soil fertility susceptibility index (SFSI) ranged from 0.64 to 1.34 for tuber yield and 0.60 to 1.30 for shoot dry weight. The genotypes R034, R041, R050, R052, R060, R100, and R125 combined lower SFSI with a low rate of reduction in tuber yield were identified as tolerant to LF stress related to the soil mineral deficiency. Likewise, the genotypes R109, R119, and R131 showed high susceptibility to soil fertility level and/or fertilizer response. Genotypes R025 and R034 had the tuber yielding potential twice of that the local variety under low soil nutrient conditions. Shoot dry weight and tuber yield showed a positive correlation both under low and high soil fertility conditions (r = 0.69 and 0.75, respectively), indicating the vigor biomass may be a morphological marker for selecting genotypes of white Guinea yam for higher tuber yield. Our results highlight genotypic variation in the tolerance to low soil nutrients and mineral fertilizer response in white Guinea yam to exploit through breeding and genetic studies to develop improved genotypes for low and high input production systems in West Africa.

Dataset Information

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

Publications

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

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