BMC Biology：幾內亞山藥的基因組被破譯
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近日，由日本研究岩手生物技術研究中心 (Iwate Biotechnology Research Center,IBRC) 的Ryohei Terauchi領導團隊破譯了白色幾內亞山藥(white Guinea yam)的基因組。該研究成果發表在《BMC Biology》上。研究結果表明幾內亞山藥的基因組大小為594Mb。利用Illumina的MiSeq和HiSeq 2500平台,生成了85.14 Gb序列，這使得基因組覆蓋度達149倍。利用組裝軟體,產生了超過4723個scaffold，估算基因組大小約為594 Mb。此外，對幾內亞山藥各個組織展開RNA-Seq, 預測出山藥基因組包含26198個基因。其中，大約發現有5557個基因在短柄草、水稻和擬南芥中有直系同源，而12625個在這些物種中沒有找到直系同源物或旁系同源基因。同時文章還研究了對決定植物是雌性還是雄性的基因組區域進行定位，對253株植物開展的QTL-seq分析結果表明，11號偽染色體上的一段區域在雄性植物中是純合的，而在雌性植物中確是雜合的。這暗示ZZ表型能穩定產生雄性植物, 而ZW表型不大穩定。它們通常是雌性植物, 但有時也會產生雌雄同株或雄性植物。
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山藥：雌雄異株
Fig.1 Determination of ploidy level and genome size inDioscorea rotundataplant
山藥是薯蕷科薯蕷屬的成員之一.在西非和中非,最受歡迎的種類是白色幾內亞山藥(Dioscorea rotundata).然而,這種植物是雌雄異株的,這可能影響了收成.在開花植物中,雌雄異株的植物大約只佔5-6%,包括山藥和蘆筍.歡迎點擊「PaperRss」關注我們！
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山藥尚未被馴化,屬於被忽視的"孤兒"作物
奈及利亞的山藥產量佔世界總產量的70%左右,但目前的消費需求量已超過其產量。破譯山藥基因組變得至關重要,因為與小麥、玉米和水稻等糧食作物不同,山藥尚未被馴化,屬於被忽視的"孤兒"作物.了解這種關鍵植物的基因組學,將有助於農民提高山藥的產量和可持續性。歡迎點擊「PaperRss」關注我們！
Fig.2 Comparative genomics ofDioscorea rotundataand other angiosperm species
Fig.3QTL-seq-based analysis of sex determination inD. rotundata
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研究意義
對山藥等孤兒作物進行基因組分析,這有助於改善糧食安全狀況以及熱帶農業的可持續性。歡迎點擊「PaperRss」關注我們！
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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