US 12,451,214 B2
Haplotype-block-based imputation of genomic markers
Adnane Nemri, Montpellier (FR); and Torsten Pook, Goettingen (DE)
Assigned to KWS SAAT SE & CO. KGAA, Einbeck (DE); and GEORG-AUGUST-UNIVERSITAET GOETTINGEN STIFTING OEFFENTLICHEN RECHTS, Goettingen (DE)
Appl. No. 18/030,602
Filed by KWS SAAT SE & CO. KGAA, Einbeck (DE); and GEORG-AUGUST-UNIVERSITAET GOETTINGEN STIFTING OEFFENTLICHEN RECHTS, Goettingen (DE)
PCT Filed Oct. 6, 2021, PCT No. PCT/EP2021/077505
§ 371(c)(1), (2) Date Apr. 6, 2023,
PCT Pub. No. WO2022/074034, PCT Pub. Date Apr. 14, 2022.
Claims priority of application No. 20201121 (EP), filed on Oct. 9, 2020.
Prior Publication US 2023/0368864 A1, Nov. 16, 2023
Int. Cl. G16B 20/00 (2019.01); G16B 35/00 (2019.01); G16H 50/30 (2018.01)
CPC G16B 20/00 (2019.02) [G16B 35/00 (2019.02); G16H 50/30 (2018.01)] 14 Claims
OG exemplary drawing
 
1. A method for predicting a genome-related feature from genomic marker data of multiple individuals, the method comprising:
receiving, at a computing device, genomic marker data of each of the individuals, the multiple individuals comprising one haplotype or multiple haplotypes respectively, the genomic marker data of an individual being indicative of a plurality of marker positions in the genome of the individual, wherein first ones of the marker positions are respectively assigned to a marker variant identified at this first marker position, wherein multiple second ones of the marker positions have a missing or ambiguous marker variant assignment;
computing, at the computing device, a haplotype-block library comprising a plurality of haplotype-blocks, each haplotype-block comprising start and stop coordinates and a series of marker positions referred to as ‘comparison marker positions’ lying within the start and stop coordinates;
performing, at the computing device, a haplotype-block-guided marker imputation of marker variants at the second marker positions selectively within genomic sub-regions whose start and stop coordinates correspond to the start and stop coordinates of one or more of the haplotype-blocks, whereby the imputation is computed as a function of marker variants comprised in the genomic sub-regions of a sub-set of the haplotypes, the haplotypes of the sub-set of the haplotypes comprising the one or more haplotype-blocks;
supplementing, at the computing device, the genomic marker data of the multiple individuals by assigning the imputed marker variants to respective ones of the second marker positions;
using, at the computing device, the supplemented genomic marker data for computationally predicting the feature of the individuals; and
conducting a plant or animal breeding project by:
providing a group of candidate plant or animal individuals, wherein a candidate individual is a respective individual potentially to be used in the breeding project, the feature being indicative of a breeding value of the candidate individuals or their offspring; and
selecting and using ones of the candidate individuals as parent individuals in the breeding project whose predicted breeding value is the highest.