近日，由日本研究岩手生物技术研究中心 (Iwate Biotechnology Research Center,IBRC) 的Ryohei Terauchi领导团队破译了白色几内亚山药(white Guinea yam)的基因组。 该研究成果发表在《BMC Biology》上。研究结果表明几内亚山药的基因组大小为594Mb。利用Illumina的MiSeq和HiSeq 2500平台,生成了85.14 Gb序列，这使得基因组覆盖度达149倍。利用组装软件,产生了超过4723个scaffold，估算基因组大小约为594 Mb。此外，对几内亚山药各个组织展开RNA-Seq, 预测出山药基因组包含26198个基因。其中，大约发现有5557个基因在短柄草、水稻和拟南芥中有直系同源，而12625个在这些物种中没有找到直系同源物或旁系同源基因。同时文章还研究了对决定植物是雌性还是雄性的基因组区域进行定位，对253株植物开展的QTL-seq分析结果表明，11号伪染色体上的一段区域在雄性植物中是纯合的，而在雌性植物中确是杂合的。这暗示ZZ表型能稳定产生雄性植物, 而ZW表型不大稳定。它们通常是雌性植物, 但有时也会产生雌雄同株或雄性植物。
Fig.1 Determination of ploidy level and genome size in Dioscorea rotundata plant
山药是薯蓣科薯蓣属的成员之一.在西非和中非,最受欢迎的种类是白色几内亚山药(Dioscorea rotundata).然而,这种植物是雌雄异株的,这可能影响了收成.在开花植物中,雌雄异株的植物大约只占5-6%,包括山药和芦笋.欢迎点击「PaperRss」↑关注我们！
尼日利亚的山药产量占世界总产量的70%左右,但目前的消费需求量已超过其产量。破译山药基因组变得至关重要,因为与小麦、玉米和水稻等粮食作物不同,山药尚未被驯化,属于被忽视的"孤儿"作物.了解这种关键植物的基因组学,将有助于农民提高山药的产量和可持续性。欢迎点击「PaperRss」↑关注我们！
Fig.2 Comparative genomics of Dioscorea rotundata and other angiosperm species
Fig.3 QTL-seq-based analysis of sex determination in D. rotundata
对山药等孤儿作物进行基因组分析,这有助于改善粮食安全状况以及热带农业的可持续性。欢迎点击「PaperRss」↑关注我们！
Title： 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.
Keywords
Yam Dioscorea Whole-genome sequence Dioecy Sex determination
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