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

该项目将开发豆类和油籽作物基因组选择技术，方法是将罗斯林为牲畜计算遗传学和育种计划设计开发的研究工具应用于花生育种计划。基因组选择已经彻底改变了全世界的牲畜育种计划，因为动物是根据基因型信息（可以从非常年轻的动物身上收集）而不是准确的表现型信息（遗传特征）来选择育种的，而表现型信息可能要到出生后几年才能获得。基因组选择现在广泛而成功地应用于奶牛、猪、羊和家禽，它为提高植物育种计划的效率、有效性和可持续性提供了新的机会。基因组选择在脉冲育种中所带来的好处与在家畜育种中所带来的好处是一样的。育种计划中的遗传改良率由四个因素决定：选择强度、选择准确性、育种周期时间和可供选择的遗传多样性的数量。前三个因素将通过基因组选择得到改善。在本讨论中，我们以花生为例，但非常类似的限制也适用于其他油籽和豆类作物。选择强度低，育种周期时间长，因为诸如X、Y、产量和抗病性等性状以及受环境相互作用影响的基因型只能在育种周期的后期进行选择，此时大多数候选品种在粗略的视觉标准下已被淘汰。一旦开发出低成本的基因分型技术，基因组选择将允许在大量植物中估计所有性状。我们需要低成本的基因分型技术来增加选择强度。选择的准确性是有限的，因为在育种周期的前几年，选择仅限于在苗期可以测量的少数性状。产量、X、环境相互作用的基因型和Y等重要因素无法在幼苗中进行评估。一旦创建了适当的训练种群并收集了必要的表型和基因型数据，基因组选择将允许在幼苗中以高度准确的方式估计所有重要性状的育种值。我们需要对训练人群进行优化设计，以提高选择的准确性。花生的育种周期时间至少为4年，因为从杂交到从F1到F6的进代需要时间才能达到纯合性，从而可以在小区中进行表型分析。基因组选择可以将育种周期缩短到1年甚至6个月，因为基因组选择可以在未成熟的幼苗上进行，因此通过快速的世代推进，一旦选择候选者成熟，就可以开始新的周期。此外，基因组选择也有助于从F3代开始减小大小，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，因为它可能使遗传改良率提高10倍。我们需要优化育种计划设计和过渡策略，以一种负担得起的方式减少育种周期时间，从而将风险降到最低，因此需要拟议的研究。为了实现这个项目，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限制下产生足够的基因组数据。我们需要开发一个基因组选择训练集。我们需要开发和优化重新设计的育种计划中的种群改进和产品开发组成部分。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.