Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops

被引：24

作者：

Gemenet, Dorcus C. ^{[1
,4
]}

Lindqvist-Kreuze, Hannele ^{[2
]}

De Boeck, Bert ^{[2
]}

Pereira, Guilherme de Silva ^{[1
,3
]}

Mollinari, Marcelo ^{[3
]}

Zeng, Zhao-Bang ^{[3
]}

Yencho, G. Craig ^{[3
]}

Campos, Hugo ^{[2
]}

机构：

[1] Int Potato Ctr, ILRI Campus,POB 25171-00603, Nairobi, Kenya

[2] Int Potato Ctr, Av La Molina 1895, Lima, Peru

[3] North Carolina State Univ, Raleigh, NC 27695 USA

[4] Int Maize & Wheat Improvement Ctr CIMMYT, CGIAR Excellence Breeding Platform, ICRAF Campus, Nairobi 104100621, Kenya

来源：

THEORETICAL AND APPLIED GENETICS | 2020年 / 133卷 / 12期

基金：

比尔及梅琳达.盖茨基金会;

关键词：

ALLELE FREQUENCIES; PREDICTION; POLYPLOIDS; COVARIANCE; VARIANCE;

D O I：

10.1007/s00122-020-03673-2

中图分类号：

S3 [农学（农艺学）];

学科分类号：

0901 ;

摘要：

Key message Polypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture. The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparentalF(1)population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; <= 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.

引用

页码：3345 / 3363

页数：19