Genotyping by Sequencing for SNP-Based Linkage Analysis and the Development of KASPar Markers for Male Sterility and Polyembryony in Citrus

Abstract

Polyembryony and male sterility (MS) are essential characters for citrus breeding. MS, coupled with parthenocarpy, allows for addressing the diversification of diploid seedless mandarin varieties, and nucleocytoplasmic MS is the most prevalent system. Polyembryony limits the use of seed parents in scion breeding programs, and the recovery of monoembryonic hybrids to be used as female parents is a crucial pre-breeding component. The objectives of this work were the identification of SNPs closely linked with the genes implied in these traits for marker-assisted selection. Genotyping by sequencing was used to genotype 61 diploid hybrids from an F1 progeny recovered from crossing ‘Kiyomi’ and ‘Murcott’ tangors. A total of 6444 segregating markers were identified and used to establish the two parental genetic maps. They consisted of 1374 and 697 markers encompassing 1416.287 and 1339.735 cM for ‘Kiyomi’ and ‘Murcott’, respectively. Phenotyping for MS and polyembryony was performed. The genotype–trait association study identified a genomic region on LG8 which was significantly associated with MS, and a genomic region on LG1 which was significantly associated with polyembryony. Annotation of the identified region for MS revealed 19 candidate genes. One SNP KASPar marker was developed and fully validated for each trait.

Inheritance and Quantitative Trait Loci Mapping of Aromatic Compounds from Clementine (Citrus × clementina Hort. ex Tan.) and Sweet Orange (C. × sinensis (L.) Osb.) Fruit Essential Oils

“…QTLs vary among studies, as well as over the fruit-ripening period. This complexity of quality trait inheritance can explain why, compared with that in other crops, marker-assisted selection is still limited in citrus to a few traits with monogenic determinants, such as Alternaria brown spot resistance [ 62 ], Tristeza immunity of Poncirus trifoliata (L.) Raf., polyembryony or male sterility [ 63 ]. On the other hand, markers for QTLs of aromatic compounds can be used to vary the content of compounds and create new aroma profiles.…”

Advancing tree genomics to future proof next generation orchard production

“…MAS allows breeders to screen large populations during the seedling stage and select those with the potential to exhibit the desired traits at maturity. For example, in citrus a hybrid population of 'Kiyomi' and 'Murcott' tangors segregating for male sterility and polyembryony was used to develop and validate markers tightly linked to both traits to be used for MAS in breeding programs (Montalt et al, 2023). In macadamia, the identification of markers tightly linked to nut quality characteristics could be used to screen for elite progeny potentially reducing the selection process by seven years in the breeding program (O'Connor et al, 2019).…”

“…Consequently, GS has the potential to enable breeders to accurately estimate the performance of trees before they reach maturity, allowing for early identification of top-performing individuals. (Shen et al, 2019) Disease resistance in trifoliate orange (Peng et al, 2020) HLB tolerance in 'Argentina' and 'Flying Dragon' trifoliate orange and 'Sanford' and 'Succari' sweet orange (Huang M. et al, 2023) Male sterility and polyembryony in 'Kiyomi' and 'Murcott' mandarin (Montalt et al, 2023) Fruit weight in 'Tommy Atkins' x 'Kensington Pride' hybrids (Bally et al, 2021) Anthracnose resistance in 143 mango varieties (Felipe et al, 2022) Fruit colour and firmness in 'Amrapali'/ 'Sensation' hybrids (Srivastav et al, 2023)…”