Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome-specific KASP genotyping assays

Abstract

27For future food security it is important that wheat, one of the most widely consumed crops 28 in the world, can survive the threat of abiotic and biotic stresses. New genetic variation is 29 currently being introduced into wheat through introgressions from its wild relatives. For 30 trait discovery, it is necessary that each introgression is homozygous and hence stable. 31Breeding programs rely on efficient genotyping platforms for marker-assisted selection 32 (MAS). Recently, single nucleotide polymorphism (SNP) based markers have been made 33 available on high-throughput Axiom ® SNP genotyping arrays. However, these arrays are 34 inflexible in their design and sample numbers, making their use unsuitable for long-term 35 MAS. SNPs can potentially be converted into Kompetitive allele-specific PCR (KASP™) 36 assays which are comparatively cost-effective and efficient for low-density genotyping of 37 introgression lines. However, due to the polyploid nature of wheat, KASP assays for 38 homoeologous SNPs can have difficulty in distinguishing between heterozygous and 39 homozygous hybrid lines in a backcross population. To identify co-dominant SNPs, that 40 can differentiate between heterozygotes and homozygotes, we PCR-amplified and 41 sequenced genomic DNA from potential single-copy regions of the wheat genome and 42 compared them to orthologous copies from different wild relatives. A panel of 620 43 chromosome-specific KASP assays have been developed that allow rapid detection of wild 44relative segments and provide information on their homozygosity and site of introgression 45 in the wheat genome. A set of 90 chromosome-nonspecific assays was also produced that 46 can be used for genotyping introgression lines. These multipurpose KASP assays represent 47 a powerful tool for wheat breeders worldwide. 48 49

Variation in key leaf photosynthetic traits across wheat wild relatives is accession dependent not species dependent

“…These steps are not linear, and one process may inform the discovery of another. One of the limiting factors has been the inability to rapidly genotype large numbers of lines, but this has recently been overcome (King et al ., 2017; Devi et al ., 2019; Grewal et al ., 2020). Another significant bottleneck has been the availability of sophisticated high‐throughput photosynthesis phenotyping tools.…”

Fine mapping PsPS1, a gene controlling pod softness that defines market type in pea (Pisum sativum)

“…The KASP molecular marker that were developed and identified to be tightly linked with PsPS1 , for instance, KaSP‐10–KaSP‐14 , will facilitate early‐stage and precise selection of the target traits through marker‐assisted selection to accelerate the breeding process. Compared with other types of DNA markers such as SSR that are currently used in pea (Singh et al, 2015), KASP represents a new generation marker technology, which can be used to analyse single nucleotide polymorphisms and has the advantages of high accuracy, flexibility and low cost (Bello et al, 2014; Chai et al, 2021; Grewal, Hubbart‐Edwards, et al, 2020; Grewal, Othmeni, et al, 2020). In pea, KASP markers have been used for the study of resistance to Mosaic Virus Pathotype P1 (Swisher Grimm & Porter, 2020), powdery mildew (Ma et al, 2017), ascochyta blight (Jha et al, 2019), and salt tolerance (Javid et al, 2015).…”

Resistance to wheat rusts identified in wheat/Amblyopyrum muticum chromosome introgressions

“…muticum and the application of new marker technology, over 200 introgressions have been generated between wheat and Am. muticum (Dover & Riley, 1972; King et al., 2017, and 2019; Grewal et al., 2019). Twenty‐four of the 28 lines evaluated here carry single introgressions with the remaining four carrying either two or three.…”

“…From 237 Am. muticum ‐specific SNPs, 137 KASP markers have been derived that span the genome (Grewal et al., 2019; Supplemental Table S1 includes KASP markers that can be used for each line). Most importantly, two lines have small fragments that should have less linkage drag and can be useful as germplasm in breeding strategies.…”