PT  - JOURNAL ARTICLE
AU  - Guilherme da Silva Pereira
AU  - Dorcus C. Gemenet
AU  - Marcelo Mollinari
AU  - Bode A. Olukolu
AU  - Joshua C. Wood
AU  - Federico Diaz
AU  - Veronica Mosquera
AU  - Wolfgang J. Gruneberg
AU  - Awais Khan
AU  - C. Robin Buell
AU  - G. Craig Yencho
AU  - Zhao-Bang Zeng
TI  - Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population
AID  - 10.1101/622951
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 622951
4099  - http://biorxiv.org/content/early/2019/04/29/622951.short
4100  - http://biorxiv.org/content/early/2019/04/29/622951.full
AB  - In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population (‘Beauregard’ × ‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly predicted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every cM position. Multiple interval mapping was performed using our R package QTLPOLY and detected a total of 41 QTL, ranging from one to ten QTL per trait. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions allowed us to characterize additive allele effects as well as to compute QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.