Gordillo, A. | Search bioRxiv

bioRxiv2023

Identifying variants associated with dwarfism via long read sequencing of the Ddw1locus in winter rye

Dwarfism or semi-dwarfism is an established characteristic in the European cereal market, for example semi-dwarf barley and wheat are commonplace. However, dwarf winter rye is still atypical commercially and fundamental research into the underlying genes influencing plant height is still in its relative infancy. In this study, association between two independent dwarf donors are established as Ddw1 carriers and variants within the Ddw1 locus are identified using long read sequencing. Here over 20,000 variants are identified as having putative association with the dwarf phenotype by using two Ddw1 genotypes and four representative (non-dwarf) elite lines for exclusion. Consequently, the sequence data presented here provides rye breeders and researchers a resource to develop KASP markers to track the allelic status of Ddw1 and to select for dwarf material.

genomics↗

bioRxiv2022

Assessing the response to genomic selection by simulation

The goal of any plant breeding program is to maximize genetic gain for traits of interest. In classical quantitative genetics, the genetic gain can be obtained from what is known as "Breeders equation". In the past, only phenotypic data was used to compute the genetic gain. The advent of genomic prediction has opened the door to the utilization of dense markers for estimating genomic breeding values or GBV. The salient feature of genomic prediction is the possibility to carry out genomic selection with the assistance of the kinship matrix, hence, improving the prediction accuracy and accelerating the breeding cycle. However, estimates of GBV as such do not provide the full information on the number of entries to be selected as in the classical response to selection. In this paper, we use simulation, based on a fitted mixed model for genomic prediction in a multi-environmental framework, to answer two typical questions of a plant breeder: (1) How many entries need to be selected to have a defined probability of selecting the truly best entry from the population; (2) What is the probability of obtaining the truly best entries when some top-ranked entries are selected.

genetics↗