A strategy to exploit genomic selection for achieving higher genetic gains in groundnut

该项目将开发豆类和油料作物的基因组选择技术，将罗斯林开发的用于家畜计算遗传学和育种方案设计的研究工具应用于花生育种方案。基因组选择使世界各地的家畜育种计划发生了革命性的变化，因为动物是根据基因信息--可以从非常年轻的动物身上收集--而不是准确的表型信息(遗传特征)--选择进行繁殖的，而准确的表型信息可能要到出生后几年才能获得。基因组选择现在被广泛并成功地应用于奶牛、猪、羊和家禽，它为提高植物育种计划的效率、效力和可持续性提供了新的机会。基因组选择有望在脉冲育种中带来与在家畜中已经实现的相同的好处。育种计划中的遗传改进率由四个因素决定：选择强度、选择精度、育种周期时间和要选择的遗传多样性的数量。这些因素中的前三个将通过基因组选择得到改善。在讨论中，我们以花生为例，但在其他油料作物和豆类作物中也存在非常类似的限制。选择强度低，育种周期长，因为诸如X、Y、产量和抗病等性状以及品种与环境的互作只能在育种周期的后期进行选择，到那时，大多数候选者已经根据粗略的视觉标准被淘汰。一旦开发出低成本的基因分型技术，基因组选择将允许在非常大量的植物中估计所有特征。我们需要低成本的基因分型技术来增加选择强度。由于育种周期早期的选择仅限于苗期可以测量的少数几个性状，因此选择的准确性有限。重要的因素，如产量、X、品种与环境的交互作用和Y不能在苗木中评估。一旦建立了适当的训练群体并收集了必要的表型和基因数据，基因组选择将使所有重要性状的育种值在幼苗中得到高度准确的估计。我们需要训练群体的优化设计来提高选择的准确性。花生的育种周期至少为四年，因为从杂交到提前世代从F1到F6需要一段时间才能达到纯合子，从那里可以在小区中进行表型鉴定。由于基因组选择可以在未成熟的幼苗上进行，因此可以将育种周期缩短到一年甚至六个月，因此新的选择周期可以通过快速的世代推进在选择候选者达到成熟时立即启动。此外，基因组选择还有助于从F3代开始缩小大小，从而优化资源。与传统的花生育种相比，这种世代间隔的缩短代表了基因组选择最明显的优势，因为它使遗传改良率潜在地提高了10倍。我们需要优化的育种计划设计和过渡策略，以负担得起的方式缩短育种周期，将风险降至最低，因此有必要进行拟议的研究。为了实现这一项目，我们需要开发基因分型和测序技术、算法和策略，以便在花生育种计划的经济约束下产生足够的基因组数据。我们需要开发一套基因组选择训练集。我们需要开发和优化拟议的重新设计的育种计划的种群改进和产品开发部分。最后，我们需要在ICRISAT、DGR和UAS育种计划中实施新设计，并测试其性能。

This project will develop the technology for genomic selection in legume and oilseed crops by applying the research tools developed at Roslin for computational genetics and breeding programme design in livestock to groundnut breeding programmes. Genomic selection has revolutionised livestock breeding programmes worldwide because animals are selected for breeding on the basis of genotype information - which can be collected from very young animals - instead of accurate phenotype information (inherited characteristics) which may not be available until several years after birth. Genomic selection is now widely and successfully used in dairy cattle, pigs, sheep, and poultry and it offers new opportunities to increase the efficiency, effectiveness and sustainability of plant breeding programmes. Genomic selection promises the same benefits in pulse breeding as it has already delivered in livestock. Rates of genetic improvement in a breeding programme are determined by four factors: selection intensity, selection accuracy, breeding cycle time, and the amount of genetic diversity to be selected upon. The first three of these factors would be improved by genomic selection. In this discussion, we take the groundnut as an example but very similar limitations apply in other oilseed and pulse crops.Selection intensity is low and breeding cycle time is long because traits such as X, Y, yield and disease resistance, as well as genotype by environment interactions, can only be selected upon late in the breeding cycle, by which point most of the candidates have been eliminated on crude visual criteria. Genomic selection would allow all traits to be estimated in very large numbers of plants once low-cost genotyping technologies have been developed. We need low cost genotyping technologies to increase selection intensity.Selection accuracy is limited because selection in the early years of the breeding cycle is limited to the few traits that can be measured at the seedling stage. Important factors such as yield, X, genotype by environment interactions and Y cannot be evaluated in seedlings. Genomic selection would allow breeding values for all traits of importance to be estimated in young seedlings with a high degree of accuracy once an appropriate training population has been created and the necessary phenotype and genotype data collected. We need optimal designs for training populations to increase selection accuracy.Breeding cycle time in groundnut is a minimum of four years because of the time it takes from crossing to advance generation from F1 to F6 to achieve homozygosity from where phenotyping can be done in plots. Genomic selection could reduce the breeding cycle time to a year or even six months because genomic selection can be carried out on immature seedlings and so the new cycle can be initiated as soon as the selection candidates reach maturity through rapid generation advancement. Additionally, genomic selection also help to reduce the size from F3 generation onwards thus optimizing the resources. This reduction in generation interval represents the most obvious advantage of genomic selection in comparison to traditional groundnut breeding as it gives a potential tenfold increase in the rate of genetic improvement. We need optimised breeding programme designs and transition strategies to reduce breeding cycle time in an affordable way that minimizes risks, hence the need for the proposed research.To deliver this project we need to develop genotyping and sequencing technologies, algorithms and strategies to enable sufficient genomic data to be generated within the economic constraints of groundnut breeding programs. We need to develop a genomic selection training set. We need to develop and optimise the population improvement and product development components of the proposed redesigned breeding program. Finally, we need to implement the new design in the ICRISAT, DGR and UAS breeding programmes and test its performance.