Onion Breeding and Genetics
Mapping of the Onion Genome
Genetics of Important Production, Flavor, and Health-Enhancing Attributes of Onion
Molecular-Facilitated Selection of Maintainer Lines in Onion
Cucurbit Organellar Genetics
Stakeholder Research Priorities
Onion Breeding and Genetics
The USDA onion-breeding program uses classical and molecular approaches for the genetic improvement of onion. In an average year, we plant over 700 four-meter observation plots to produce and evaluate bulbs for inbred development, genetic studies, and seed increases. We are grateful to Gary and Corey Kincaid, Palmyra WI, for providing field space every year. Bulbs are harvested in the fall, vernalized over the winter, evaluated for desirable attributes or genetic characteristics in the spring, and planted for seed production at the Horticulture Research Farm near Arlington, WI. We generally plant 15 to 30 cages (larger seed increases or testcrosses) and 200 breeding plots (small self or mass pollinations) each year. Our crosses and seed increases are done using flies. From our breeding efforts, in 1999 we released three male-sterile and maintainer pairs (B1717, B1828, and B2354) for use in hybrid production. In 2007 we released the first male-sterile and maintainer inbred (B8667) of red onion, a male-sterile and maintainer pair (Ski-1) selected from the very early Japanese population ‘Sapporo-Ki’, and a synthetic population (OH-1) with the highest reported level of gynogenic haploid production. The vast majority of hybrid-onion seed is produced using a source of cytoplasmic male-sterility (CMS) that traces back to a single plant identified in 1925 in Davis, CA, representing an undesirable state of cytoplasmic uniformity. In 1999, we released a unique source of CMS, conditioned by the cytoplasm of Allium galanthum backcrossed to the bulb onion. The benefit of this new alloplasmic source of CMS is that no anthers are produced, making rouging in the field easier. In addition, there are no known nuclear male-fertility restorers. We also work to identify and molecularly tag tolerances to major pests of onion, including the insect thrips, Iris yellow spot virus, and fungi causing pink root and Fusarium basal rot.
Even though the onion is the world’s second most economically important vegetable crop, little is known about its progenitor, relationships to wild relatives, and genetic diversity. We used molecular markers in the organellar and nuclear genomes to identify Allium vavilovii as the wild species most closely related to the bulb onion. We cooperated with researchers in Turkmenistan to expand the world’s collection of this important wild species and deposit accessions into the US plant germplasm collection.
With support of major grants from the USDA NRI, IFAFS, and SCRI programs, we developed the most detailed genetic maps of onion, comprised of morphological, RFLP, SSR, and SNP markers, as well as the first deep sequencing of expressed regions of the onion genome. Our goal is to develop genomic resources to answer basic questions in onion genetics and breeding.
We analyzed onion pungency, storage ability, soluble-solids contents, and in vitro antiplatelet activity. This latter attribute measures the ability of onion to inhibit the aggregation of platelets in blood, a major cause of heart attacks and strokes. We identified major chromosome regions explaining a significant proportion of the phenotypic variation for flavor, solids, and antiplatelet activity. Our long-term goal is to develop unique inbreds and hybrids for production of onion bulbs with acceptable flavor and production characteristics combined with defined heath-enhancing attributes.
Using classical crosses, it takes at least four to eight years to determine the cytoplasm and nuclear genotype at the male-fertility restoration (Ms) locus of onion. We have developed PCR-based markers distinguishing male-fertile and male-sterile cytoplasms of onion, reducing from years to a few hours the time required to establish cytoplasms. We also identified single nucleotide polymorphisms (SNPs) tightly linked to Ms for easy detection.
The mitochondrial DNAs of cucumber and melon are unique in that they are among the largest known and show paternal transmission. We characterized the molecular basis of this huge genome expansion and revealed that short, highly repetitive, dispersed sequences contributed significantly to the expansion of the cucumber mitochondrial genome. In a collaborative project, we used FISH analyses to reveal great structural diversity in the chloroplast DNA and the publication from this study was awarded “Best Paper in The Plant Cell” for the year 2001. We are also studying the genetic bases of unique mitochondrial mutants of cucumber that condition strongly mosaic (MSC) phenotypes, and a nuclear locus (Psm) that controls sorting of paternally transmitted mitochondrial DNAs.