Iwate Biotechnology Research Center, Kitakami, Japan.
The Earlham Institute, Norwich, UK.
BMC Biol. 2017 Sep 19;15(1):86. doi: 10.1186/s12915-017-0419-x.
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.
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.
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.
根和块茎作物是热带非洲的主要食物来源。在这些作物中，单子叶植物薯蓣属中有几个物种统称为山药，这是一种主要的块茎作物，为数百万人民的生计和社会文化生活做出了巨大贡献，主要在西非和中非。山药的种植受到多种因素的限制，可以说山药是一种被忽视的“孤儿”作物，需要通过作物改良措施来加以改善。然而，缺乏遗传和基因组工具阻碍了这种主要作物的改良。
为了加速山药的分子标记辅助育种，我们对白薯蓣（Dioscorea rotundata）进行了基因组分析，组装了一个 594-Mb 的基因组，其中 76.4%的基因组分布在 21 个连锁群中。总共预测了 26198 个基因。用 2381 个保守基因进行系统发育分析表明，薯蓣是单子叶植物中一个独特的谱系，与禾本科（水稻）、棕榈科（棕榈）和姜科（香蕉）不同。整个薯蓣属的特征是雌雄异株（雌雄异株），这一特征限制了山药的高效繁殖。为了推断性别决定的遗传基础，我们对雌雄植株分离的 F1 后代进行了全基因组重测序（数量性状位点测序[QTL-seq]），并鉴定出与雌性异型配子（雄性=ZZ，雌性=ZW）性别决定相关的基因组区域。我们进一步划定了 W 基因座，并利用它开发了一种在苗期鉴定几内亚山药植物性别的分子标记。
几内亚山药属于单子叶植物中一个独特且高度分化的分支。本研究进行的基因组分析和性连锁标记的开发将极大地加速几内亚山药的分子标记辅助育种。此外，我们的 QTL-seq 方法可用于遗传研究其他异花授粉作物和高度杂合基因组的生物体。对山药等孤儿作物的基因组分析促进了提高粮食安全和热带农业可持续性的努力。
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