Current status and prospects of molecular marker development for systematic breeding program in citrus

Abstract

Citrus is an economically important fruit crop widely growing worldwide. However, citrus production largely depends on natural hybrid selection and bud sport mutation. Unique botanical features including long juvenility, polyembryony, and QTL that controls major agronomic traits can hinder the development of superior variety by conventional breeding. Diverse factors including drastic changes of citrus production environment due to global warming and changes in market trends require systematic molecular breeding program for early selection of elite candidates with target traits, sustainable production of high quality fruits, cultivar diversification, and cost-effective breeding. Since the construction of the first genetic linkage map using isozymes, citrus scientists have constructed linkage maps using various DNA-based markers and developed molecular markers related to biotic and abiotic stresses, polyembryony, fruit coloration, seedlessness, male sterility, acidless, morphology, fruit quality, seed number, yield, early fruit setting traits, and QTL mapping on genetic maps. Genes closely related to CTV resistance and flesh color have been cloned. SSR markers for identifying zygotic and nucellar individuals will contribute to cost-effective breeding. The two high quality citrus reference genomes recently released are being efficiently used for genomics-based molecular breeding such as construction of reference linkage/ physical maps and comparative genome mapping. In the near future, the development of DNA molecular markers tightly linked to various agronomic traits and the cloning of useful and/or variant genes will be accelerated through comparative genome analysis using citrus core collection and genome-wide approaches such as genotyping-by-sequencing and genome wide association study.

Identification of ‘Haryejosaeng’ mandarin by multiplex SNP genotyping

“…Most citrus cultivars reproduce by sexual hybridization, frequent somatic mutation, and nucellar polyembryony; the latter is a feature of citrus in which the nucellar tissue that surrounds the embryonic sac containing the zygotic embryo develops one or more embryos that have the same genetic constitution as the maternal tissue cells [32,[51][52][53]. Satsuma mandarin cultivars have been particularly difficult to improve through hybridization because of polyembryony and male sterility [3,54].…”

Genome-wide identification and expression profiling of the pectin methylesterase gene family in Citrus sinensis (L.) Osbeck

“…The average haploid genome size in citrus species ranges from 360 Mb (mandarin) to 398 Mb (citron) (Gmitter et al 2012), and several reference genomes are currently available (https://www.citrusgenomedb.org/). Citrus has several fascinating botanical features, such as long juvenility, self-/crossincompatibility, sterility in pollen/ovule, polyembryony, and high citrus-specific flavonoid content in the fruits (Kim et al 2016;Woo et al 2020), which attract scientists to study its growth and development. In this study, we identify PME gene family members with diverse functional roles from the sweet orange genome and characterize their molecular features, including molecular phylogeny and gene structure analyses.…”

Evaluation of polyembryony for genetic resources and efficacy of simple sequence repeat markers for the identification of nucellar and zygotic embryo-derived individuals in citrus

“…Simple sequence repeats (SSRs) are highly informative DNA markers due to their high degree of polymorphism and co-dominant mode of inheritance and genome-wide distribution. SSR markers have been successfully used for the identification of zygotic seedlings or nucellar rootstock candidates for rootstock breeding programs [12][13][14]. However, these previous studies used seedling populations derived from a very limited number of genetic crosses.…”