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

Abstract

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. Abstract 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 biparental F1 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.

Breeding Progress for Vitamin A, Iron and Zinc Biofortification, Drought Tolerance, and Sweetpotato Virus Disease Resistance in Sweetpotato

“…This explains the observed correlation levels and provides genetic basis to improve more than one trait concurrently. These loci can be investigated further for putative genes and markers linked to haplotypes of interest for marker-assisted selection, or for leveraging QTL-informed genomic prediction models (Gemenet et al, 2020b). However, these strategies need to be validated in populations with broader genetic bases.…”

Development of a Panel of Genotyping-in-Thousands by Sequencing in Capsicum

“…We then established conditions for library preparation with these markers to reach high genotyping rates on either one of two sequencing platforms: Miseq or Nextseq. Reliable genotyping data in diploid plants requires a sequencing depth of at least 30 reads ( Gemenet et al, 2020 ). Based on our sequencing coverage from pooled samples, we estimate that 1,500 samples can be analyzed in one Miseq lane and 13,000 samples in one Nextseq lane for 96 target loci, each represented by one GT-seq marker.…”

Rapid identification of mutations caused by fast neutron bombardment in Medicago truncatula

“…WGS uses high coverage short reads to examine the homogeneity between the reference genome and short reads. Sequencing depth is an important parameter that determines the sensitivity and reproducibility in detecting variations among genomes [ 28 , 29 ]. In this work, we proposed a minimum of 20 × sequencing depth for mutation detection.…”