Agricultural Grant To Help Breed More Resilient Yams in West Africa
农业studies aim to increase the sustainability, productivity and nutritional density of vital crop and livestock species. Illumina’s Agricultural Greater Good Initiative Grant is an award designed to boost research in this field with the end goal of reducing malnutrition, hunger and poverty by improving crop yields and enhancing livestock welfare and productivity.
2022年的赠款获胜者是Dr. Ranjana Bhattacharjee，分子遗传学家国际热带农业学院(IITA) in Ibadan, Nigeria. Her research aims to tackle food insecurities in Western Africa by studying yam species (a major food source in this region) usingwhole-genome sequencing。
捷克葡萄牙直播与Bhattacharjee进行了交谈，以了解有关山药物种的遗传分析如何提高农作物产量并产生这种研究不足的作物的更多弹性品种的更多信息。
莎拉·惠兰（Sarah Whelan）（SW）：您能告诉我您的研究和实验室中工作的重点吗？
Ranjana Bhattacharjee（RB）：I am a plant breeder and molecular geneticist, and the focus of my research is on using molecular markers and genomics-assisted breeding. My area of expertise is in yams and cacao, as well as other crops like taro and coffee. Most of the time, it is very difficult to make any changes to crop traits of interest like yield or disease resistance using conventional methods. This is when we use genomics or genome-wide associations to understand these traits of interest and make changes based on genomics.
SW：这个新项目专注于山药。您能解释山药在农业上的重要性和作为食物来源吗？
RB：首先，我想说的是，在诸如美国之类的地方，山药经常与地瓜混淆。但是，它们是属于两个不同家庭的两种不同的农作物。地瓜是ipomoea batatas，山药属于该属Dioscorea。There are 600 species of yams found all over the world covering Asia, Africa, Latin America, Oceania and the Pacific. Out of these 600 species, approximately 10 are cultivated, such asDioscorea rotundata，，，，Dioscorea cayenensis和Dioscoria alata。
由于山药是如此普遍，因此对于近300万人来说，它们作为粮食安全作物非常重要。它们是拥有一到三公顷土地的小农户的主要农作物。此外，山药的生产成本很高，因此山药农民经常会出售山药以获取钱来购买其他农作物（例如木薯，玉米或米饭），这些农作物便宜得多。山药也非常丰富淀粉，据报道与其他淀粉作物相比，山药具有最低的血糖指数之一。
Yams are also an income-secured crop. There are reports that the market value is around $13.7 billion, giving yams the nickname “King of Crops” in West Africa. Furthermore, yams contain valuable secondary metabolites like diosgenin, saponins and shikimic acid. These are important ingredients for pharmaceutical companies. These metabolites can be produced synthetically but can also be sourced naturally from certain species of yam. Therefore, if these can be extracted, this can provide a very large source of income.
SW：您说今天山药农业面临的主要挑战是什么？
RB：Issues such as low yield and diseases are the major challenges. There are diseases that affect certain yam species, for example,Dioscorea alatacan develop a fungal infection caused byColtotrichum gloeosporioides称为蒽另一个山药物种，Dioscorea rotundata，可以感染病毒感染，从而导致山药马赛克疾病。两种疾病都可以将作物产量降低80％或更多。
生产成本是另一个主要挑战。由于这种农作物是葡萄藤，因此每种植物都需要粘在地面上。西非缺乏机械化使种植和收获非常密集。这些农作物是地下块茎，可以重达八或十公斤，每种植物可以产生多个块茎。另一个挑战是种子系统本身。由于山药是一种经过克隆的繁殖作物，因此农民必须将一些种植作为种子块茎的种植材料。对于农民来说，这变得非常困难，因为他们必须在明年保留种子块茎，同时还要保留一些自身的消费。
最后，需要认识到西非的山药作为优先农作物。尼日利亚是世界上最高的山药生产商，但政策制定者和政府并不认为山药是优先农作物。这使得很难获得研究的资金来改进，从遗传学和基因组学方面的速度非常慢。当我们与决策者谈论为什么他们不想优先考虑这些农作物时，他们说尼日利亚的生产是如此之高，以至于很多块茎腐烂。但是，这取决于收获后缺乏存储设施。当这些农作物未正确储存并堆叠在另一种农作物上时，会产生很多热量，块茎可能腐烂，受到昆虫的攻击，并容易受到真菌感染的影响。这意味着很多农作物可能会丢失。
SW：恭喜您获得2022年Illumina农业更大的优质赠款的奖励。您能否在这笔赠款的帮助下描述您将要执行的研究目标？
RB：This award was initially supposed to do whole genome sequencing of only 100 genotypes. However, after a lot of discussion with Illumina, I am very grateful that they have now recognized the value of this crop and allowed me to submit approximately 1000 yam genotypes, including both cultivated and wild species.
One of the major issues with yams in West Africa is that two cultivated species –Dioscorea rotundata和Dioscorea cayenensis（也称为白色山药和黄色山药） - 与野生物种一起生长。农民进入森林地区并收集野生块茎，从物理上将其培养成常规的圆柱形形状，可能需要四到五年。然后将这些块茎称为栽培的白色山药。但是，这些块茎是白色山药，黄色山药，一种野生文化的种间杂种还是完全野生的物种，存在很多困惑。如果是野生物种，那是哪种物种？因此，在这个项目中，主要目的是对许多白色，黄色和可能的野生山药进行基因组测序，这些野生山药都是一起生长的。因此，我们可以理解这些栽培和野生物种之间的遗传关系。我们将知道这些是白色山药，黄色山药还是种间杂种。
For the second aim, we will investigate the viral DNA which is integrated within the yam genome and very difficult to separate. We will perform whole genome sequencing of 100 isolates of viruses that we have extracted from the yams themselves. This will allow us to find the regions for viral resistance in the yam genome. Interestingly, we have the draft reference genome already available for the white yam, meaning we can align the sequencing data with the available draft reference genome. This will allow us to find regions of conserved resistance genes as well as genes for other important quality traits such as dry matter content and starch quality.
SW: How might this research increase the sustainability and productivity of this crop?
RB：It may not directly and immediately impact the sustainability and the production of the crop. However, in the long run, once we understand the genes that are responsible for different traits, we can perform genomics-assisted breeding and fast-track the breeding cycle.
目前，产生新的山药种类可能需要八到十年，而且品种营业额非常低。此外，当最终向农民发布改善的品种时，改善品种的采用率也很低。生产者依靠“陆地”，这是农民在当地改编的品种。从一项代谢组学研究中，我们发现陆地的味道比改善的品种要好得多。因此，当我们尝试改善一种品种时，产量与某些质量特征（如淀粉特性，矿物质和口味）之间似乎存在负相关。通过整个基因组测序，我们将能够找到负责这些特征的基因，并执行基因组学辅助育种将这些基因转移到其中一些改进的品种中。
基因组测序还将生成大量数据，因此我们需要进行大量基因挖掘，并了解这些基因是否功能。但是，这将比其他许多作物要少得多，因为其他农作物中已经了解了事情。例如，大量研究已经改善了我们对米饭的理解，大米和山药都是单子叶植物。这意味着我们可以使用我们的大米知识应用许多相同的原理来了解山药中的基因功能。综上所述，这意味着我们可能不会看到直接的好处，但是我相信在未来五到六年内，这可能会对提高的可持续性和生产率产生重大影响。
SW：您认为这笔赠款对这个相对研究的话题有多重要？
RB：I think this is the first time Illumina has given a grant towards researching a crop that is very important to West Africa. With this grant and the publicity, already people are starting to understand that yam is its own crop and is not the same as sweet potato, so there are a lot of misunderstandings that are already being cleared up. At the same time, a lot of investors will probably now be interested in these crops. We hope that the status of the crop will change from an orphan crop to a well-researched crop with this grant. Genome sequencing is revolutionizing the world of crop improvement, and now we are adding yams to the list of crops that have undergone large-scale genome sequencing.
Dr. Ranjana Bhattacharjee was speaking to Sarah Whelan, Science Writer for Technology Networks.
