Onion Breeding and Genetics
We maintain an onion-breeding program and are committed to the genetic improvement of onion using classical and molecular approaches. 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 Kincaid, Palmyra WI, for providing field space every year. For seed production, bulbs harvested the previous year are selected based on desired attributes or defined genetic relationships and planted at Madison, WI, to produce seed. We generally plant at least 30 cages (larger seed increases or testcrosses) and 200 breeding plots (small self or mass pollinations). Our crosses and seed increases are primarily done using flies. We recently released three male-sterile and maintainer pairs (B1717, B1828, and B2354) for use in hybrid production. We have studied the combining abilities among onion populations (J. Amer. Soc. Hort. Sci. 121:604-608), estimated their relatedness using molecular markers (Theor. Appl. Genet. 90:607-614; J. Amer. Soc. Hort. Sci. 120:752-758), and established the genetic basis of seed yield (J. Amer. Soc. Hort. Sci. 126:575-578). 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. This is an undesirable state of cytoplasmic uniformity. We identified molecular markers distinguishing onion cytoplasms and assessed cytoplasmic diversity (Theor. Appl. Genet. 86:128-134, J. Amer. Soc. Hort. Sci. 119:90-93, Theor. Appl. Genet. 90:263-268). We demonstrated that two distinct types of onion CMS exist and showed that identical sources of CMS have been independently isolated and exploited around the world (Theor. Appl. Genet. 101:778-782). We released a unique source of CMS, conditioned by the cytoplasm of Allium galanthum backcrossed to the bulb onion (J. Amer. Soc. Hort. Sci. 124:626-629)


Onion Phylogenetics
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 (Plant Syst. Evol. 183:17-31, Gen. Res. Crop Evol. 44:307-313) and nuclear (Amer. J. Bot. 82:1455-1462) genomes to identify Allium vavilovii as the wild species most closely related to the bulb onion. We are cooperating with researchers in Turkmenistan to expand the world's collection of this important wild species.

 

Mapping the Onion Genome
We have developed a low-density genetic map of onion, comprised of morphological, RFLP, and RAPD markers (Theor. Appl. Genet. 96:52-62) and developed the first set of onion ESTs (Theor. Appl. Genet. 103:979-991). This work has been continued with support of a major grant from USDA-IFAFS to support EST development in onion and comparative mapping of asparagus, garlic, and onion (the most economically important crops of the monocot order Asparagales). We demonstrated that the GC characteristics of onion coding regions are more similar to the eudicots than the grasses (Plant Cell 16:114-125). Our goal is develop genomic resources for the Asparagales to answer basic questions in onion genetics and breeding. Drs. William Martin and Jernej Jakse are working on the onion-genomics project. This research is part of an on-going project on onion genetics and breeding and has been funded by the USDA and onion-seed industry.

 

Genetics of Production, Flavor, and Health-Enhancing Attributes of Onion
This is a joint cooperative project with Dr. Irwin Goldman, University of Wisconsin, and was funded by a grant from the USDA Fund for Rural America. This research was the Ph.D. project of Dr. Claudio Galmarini, who was partially funded by the National Institute for Agricultural Research (INTA) from Argentina. Replicated plantings of F2-derived F3 massed onion families produced bulbs over at least four environments. We are analyzing onion flavor (pungency), storage ability, solids (soluble and total), 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. A low density genetic map of onion was used to determine the genetic bases of these flavor, production, and health-enhancing attributes of onion. We identified one major chromosome region explaining a significant proportion of the phenotypic variation for flavor, solids, and antiplatelet activity (Mol. Gen. Genomics 265:543-551). We are presently identifying candidate genes mapping to this important position in the onion genome. Steve Raines has joined our lab and will be continuing this research. 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.

 

Molecular-Facilitated Selection of Maintainer Lines in Onion
Using classical crosses, it takes at least four to eight years to determine the cytoplasm and nuclear genotype at the Ms locus of onion. We have developed a PCR marker distinguishing male-fertile and male-sterile cytoplasms of onion (Theor. Appl. Genet. 90:263-268), reducing from years to a few hours the time required to establish cytoplasms. We identified molecular markers flanking the nuclear Ms locus at 1.9 and 8.1 cM (in press in JASHS). We identified single nucleotide polymorphisms (SNPs) in the genomic sequence of the most closely linked marker and converted these SNPs to PCR-based detection. (J. Amer. Soc. Hort. Sci. 127:576-582).

 

Cucurbit Organellar Genetics
The mitochondria of cucumber and melon are unique in that they possess the largest known genomes and show paternal transmission (J. Hered. 88:232-235; Theor. Appl. Genet. 97:122-128). Dr.Jason Lilly characterized the molecular basis of this huge genome expansion. Random mitochondrial fragments unique to the huge genome of cucumber have been cloned and over 50 kb of sequence generated. Small (about 100 bp), highly repetitive, dispersed sequences have contributed significantly to the expansion of this genome (Genetics 159:317-328). With our colleagues, we used FISH analyses to reveal great structural diversity in the chloroplast DNA (Plant Cell 13:245-254). The publication was awarded "Best Paper in The Plant Cell" for the year 2001. Drs. Lilly and Grzegorz Bartoszewski studied the genetic bases of unique mitochondrial mutants of cucumber conditioning strong mosaic (msc) phenotypes (Curr. Genet. 40:144-151, Curr. Genet. 45:45-53). Sulieman Al-Faifi is working to understand the mechanism of paternal transmission of the cucumber mitochondrial genome.

 

Mapping Virus Resistances in Cucumber
Genes conditioning resistance to PRSV-W and ZYMV were mapped relative to RFLPs, RAPDs, and AFLPs, using recombinant inbred lines developed from TMG1 x Straight 8. Numerous students and colleagues contributed to this work and it was completed by Young Hoon Park (Genome 43:1003-1010). We are now converting a cosegregating AFLP marker to an easier PCR-based marker and studying the synteny among virus resistance loci in the cucurbits. Neil Williams is continuing this research with support of a grant in 2003 from the USDA-NRI program.

 

Late-Blight Resistance in Mexican Diploid Solanum species
This was a joint project with the late Dr. Robert Hanneman, USDA/ARS and the University of Wisconsin, and was the Ph.D. project of Dr. Joe Kuhl. Late blight resistance and susceptibility were identified in Mexican diploid 1EBN species. Solanum pinnatisectum was crossed with the susceptible S. cardiophyllum and a BC family generated. RFLPs were identified on all chromosome arms and mapped late-blight resistance to chromosome 7 in a region not previously associated with late-blight resistance loci (Mol. Genet. Genomics 265:977-985). Monica Norby is presently studying the synteny among late-blight resistance loci in Solanum. This project has been funded by the USDA. We also showed that unilateral incompatibilities among Mexican 2x(1EBN) species is inherited independently of the S locus in Solanum (Sexual Plant Reprod. 14:305-313).