Next-generation onion (Allium cepa) breeding using molecular markers: progress and prospects--a review

Onion (Allium cepa L.) is an indispensable vegetable crop throughout the globe. It is a member of family Amaryllidaceae (formerly Alliaceae family) and is characterized by 16 somatic chromosomes and a massive 16.4 Gbp genome. Despite its economic significance, the pace of genetic improvement has historically been hindered by the complex and biennial life cycle, photosensitivity, high inbreeding depression and a lack of sufficient genomic resources. The shift from low-throughput markers like RAPD and RFLP to high-resolution and reliable marker systems like SSRs and SNPs has facilitated the construction of saturated linkage maps, leading to identification of QTLs for various traits like resistance to downy mildew, purple blotch, anthracnose and thrips, apart from tolerance to drought stress. Development of specialized mapping populations like doubled haploids has also enabled rapid fixation of heterozygosity and led to identification of responsible loci for different nutritional and bulb-quality traits. Deployment of molecular markers like PsaO, AcPMS1 for rapid identification of Cytoplasmic-Genetic Male Sterility (CGMS) systems, is paving the way for hybrid seed production in a cost-effective manner. Thus, this review synthesizes the evolution of onion breeding, transitioning from conventional phenotypic selection to modern genomic-assisted improvement to overcome the genome complexities for accelerated development of high-yielding, multi-stress-resistant onion cultivars.