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利用历史农艺数据为路易斯安那甘蔗品种开发计划中的早期克隆选择制定基因组预测策略。

Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program.

作者信息

Shahi Dipendra, Todd James, Gravois Kenneth, Hale Anna, Blanchard Brayden, Kimbeng Collins, Pontif Michael, Baisakh Niranjan

机构信息

School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA.

Sugarcane Research Unit, USDA-ARS, Houma, Louisiana, USA.

出版信息

Plant Genome. 2025 Mar;18(1):e20545. doi: 10.1002/tpg2.20545.

Abstract

Genomic selection can enhance the rate of genetic gain of cane and sucrose yield in sugarcane (Saccharum L.), an important industrial crop worldwide. We assessed the predictive ability (PA) for six traits, such as theoretical recoverable sugar (TRS), number of stalks (NS), stalk weight (SW), cane yield (CY), sugar yield (SY), and fiber content (Fiber) using 20,451 single nucleotide polymorphisms (SNPs) with 22 statistical models based on the genomic estimated breeding values of 567 genotypes within and across five stages of the Louisiana sugarcane breeding program. TRS and SW with high heritability showed higher PA compared to other traits, while NS had the lowest. Machine learning (ML) methods, such as random forest and support vector machine (SVM), outperformed others in predicting traits with low heritability. ML methods predicted TRS and SY with the highest accuracy in cross-stage predictions, while Bayesian models predicted NS and CY with the highest accuracy. Extended genomic best linear unbiased prediction models accounting for dominance and epistasis effects showed a slight improvement in PA for a few traits. When both NS and TRS, which can be available as early as stage 2, were considered in a multi-trait selection model, the PA for SY in stage 5 could increase up to 0.66 compared to 0.30 with a single-trait model. Marker density assessment suggested 9091 SNPs were sufficient for optimal PA of all traits. The study demonstrated the potential of using historical data to devise genomic prediction strategies for clonal selection early in sugarcane breeding programs.

摘要

基因组选择可以提高甘蔗(甘蔗属)的遗传增益率和蔗糖产量,甘蔗是全球重要的经济作物。我们使用20451个单核苷酸多态性(SNP),基于路易斯安那甘蔗育种计划五个阶段内和跨阶段的567个基因型的基因组估计育种值,采用22种统计模型评估了六个性状的预测能力(PA),这六个性状分别为理论可回收糖(TRS)、茎数(NS)、茎重(SW)、甘蔗产量(CY)、蔗糖产量(SY)和纤维含量(Fiber)。与其他性状相比,遗传力高的TRS和SW表现出更高的PA,而NS的PA最低。机器学习(ML)方法,如随机森林和支持向量机(SVM),在预测低遗传力性状方面优于其他方法。ML方法在跨阶段预测中对TRS和SY的预测准确率最高,而贝叶斯模型对NS和CY的预测准确率最高。考虑显性和上位性效应的扩展基因组最佳线性无偏预测模型在一些性状的PA上略有改进。当在多性状选择模型中同时考虑最早在第2阶段就可获得的NS和TRS时,与单性状模型相比,第5阶段SY的PA可提高到0.66,而单性状模型的PA为0.30。标记密度评估表明,9091个SNP足以对所有性状进行最佳PA。该研究证明了利用历史数据为甘蔗育种计划早期的克隆选择设计基因组预测策略的潜力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b941/11685804/d69188c09cd4/TPG2-18-e20545-g003.jpg

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