1
Dani Zamir: Pioneer in Tomato Genetics and Quantitative Trait Dissection

Irwin L. Goldman

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, USA

ABSTRACT

The dedicatory chapters for PBR have traditionally not had abstracts; but if there is a strong sense that there should be one I can write it- however this hasn't always been done.

KEYWORDS: Tomato, quantitative trait loci, introgression lines, tomato genome, overdominance, introgression breeding

OUTLINE

1. I. INTRODUCTION
2. II. UNDERSTANDING QUANTITATIVE GENETIC VARIATION
3. III. CLONING OF QUANTITATIVE TRAIT LOCI
4. IV. CHARACTERIZATION OF GENETIC PHENOMENA
5. V. SEQUENCING THE TOMATO GENOME
6. VI. PRACTICAL PLANT BREEDING
7. VII.SCIENTIFIC IMPACT
8. VIII. LIST OF SCIENTIFIC JOURNAL PUBLICATIONS OF DANI ZAMIR
9. ACKNOWLEDGMENTS
10. LITERATURE CITED

ABBREVIATIONS

ILs

Introgression Lines

QTL

Quantitative Trait Locus

CWR

Crop Wild Relative

I. INTRODUCTION

For more than four decades, Dani Zamir has been among the most influential scientists in plant breeding throughout the world (Figure 1.1). Professor Zamir has spent his career at the Hebrew University of Jerusalem, in Rehovot, Israel, where he and his students have made great strides in improving our understanding of the genetic basis of quantitative traits in crop plants and in developing tools for advancing the science of plant breeding. Zamir was able to combine those efforts with practical plant breeding, leading to the development of highly productive cultivars and the establishment of practical breeding programs in horticultural species. He also mentored many undergraduate and graduate students in plant genetics and taught a popular course. Now Professor Emeritus, Dani Zamir's work on tomato genomics, genetics, and breeding continues into his fifth decade of work on the crop. This dedication focuses on a few of his key accomplishments in the field of plant breeding and plant genetics.

Fig. 1.1. Dani Zamir, Professor Emeritus, Hebrew University of Jerusalem, Israel.

Source: Photo credit: D. Zamir.

Dani Zamir was born in 1950 in Israel. Following his military service, he received degrees from the Hebrew University of Jerusalem (undergraduate) and the University of California-Davis (graduate), completing his doctorate in 1981. He started his career as a lecturer in genetics at the Hebrew University's Faculty of Agriculture in Rehovot, Israel, in 1982 and was appointed senior lecturer in 1985. In 1992, he became associate professor and in 1996, professor of Genetics. He retired from his formal teaching and research at the University in 2018 and is now Professor Emeritus. Zamir also held adjunct appointments in genetics at Seoul University in South Korea and Cornell University in Ithaca, New York. Throughout his career, Zamir taught a popular course in general genetics to undergraduates at Hebrew University and was a mentor for numerous students.

Zamir has also founded two companies, each of which has achieved substantial success. The first, AB Seeds, initiated approximately 20?years ago, is a breeding and genetics company specializing in crop seeds including tomato. The company was sold to De Ruiter in 2008 and later purchased by Monsanto. More recently, Zamir and his student Yaniv Semel established the company Phenome Networks, which has developed proprietary software for managing complex breeding programs and the phenotypic and genotypic data that they generate. The company, based in Rehovot, Israel, serves a wide variety of public and private customers and helps users track crossing, trialing, phenotyping, and genotyping activities that are core components of breeding programs.

Zamir has served on the advisory boards of a number of institutions, journals, and projects, including Genoplante (France), the Max Planck Institute for Plant Breeding (Germany), the Department of Plant Molecular Biology at the University of Barcelona (Spain), the Grapevine Genome Project (Italy), the International SOL Genome Project, and the journals G3: Genes, Genomes, Genetics; Scientific Data; The Plant Journal; and Scientific Reports.

Zamir was also recipient of the Kaye Innovation Prize from the Hebrew University of Jerusalem in 2007, the EMET Prize in Agriculture in 2015, which recognizes excellence in academic and professional achievements that have significant influence on society, and the highly prestigious Israel Prize 2020. The Israel Prize is awarded by the State of Israel and is considered the highest honor the state bestows on an individual. It is highly selective and awarded annually in a formal state ceremony attended by the President, Prime Minister, and other dignitaries. The recipients of the prize are Israeli citizens or organizations who have displayed excellence in their field(s) or have contributed strongly to the culture of Israel. Receipt of this award is a singular achievement and a powerful indicator of the impact of Dani Zamir's work in agricultural science.

II. UNDERSTANDING QUANTITATIVE GENETIC VARIATION

Dani Zamir has long been a proponent of understanding and utilizing genetic variability, particularly that from crop wild relatives (CWRs), to improve modern crops. Among his most well-known projects was the development of tomato (Solanum lycopersicon) introgression lines (ILs) containing small, molecular marker-defined chromosomal segments from the wild species Solanum pennellii. His approach, which became known as Introgression Breeding, is predicated on the idea that crop domestication may have left behind useful allelic variation. In a publication that has been cited nearly 1,300 times, Eshed and Zamir (1995) argued that some of this variation may be valuable in a modern breeding context and that genetic tools could be developed to identify and introgress that variation into modern cultivars without the disadvantages of using CWRs directly as parents in a breeding program. The approach gained worldwide acclaim and has been attempted in a number of crop species. The resulting progenies from these types of approaches are called Introgression Lines, or ILs.

Zamir (2001) later suggested that a genetic infrastructure could be developed based on "exotic libraries" where individual breeding lines or cultivars in the library would contain a marker-defined chromosomal segment from a CWR that had been introgressed through sexual recombination. A full set of lines of this sort would constitute a library of the genome of the CWR, albeit nested inside the genome of cultivated crop accessions. A scientist could obtain lines from the library to screen for traits of interest and potentially identify one or more lines carrying segments with valuable traits. These lines could then be easily introgressed into breeding material or cultivars using the markers flanking the introgression. These ideas were later more fully expanded to consider how this approach could be used to source natural variation for plant breeding programs (Zamir 2008).

Zamir's key insights into the value of allelic variation in CWRs were (1) that there were ways to access their value without using their entire genome as a parent in a breeding program and (2) that the genome of the wild relative could be assembled piece by piece into a library that was based on a cultivated genetic background. Plant breeders have long been aware of the pitfalls of using CWR as parents, including substantial linkage drag with undesirable traits, introduction of sterility and incompatibility, and limited recombination between wild and cultivated chromosomes. Granted, there are numerous examples of introgressions of important alleles from CWRs into cultivated crops; though these almost always involved substantial backcrossing to the cultivated parent to remove the genome of the wild parent and retain only the small segment associated with the trait of interest. In a number of these cases, unwanted segments of wild species chromosomes remain and are difficult to remove because of limited recombination at or near the unwanted genes of interest. The IL approach circumvents this problem by pre-developing a set of marker-defined ILs and allowing for a more custom-designed breeding approach (Figure 1.2).

But of even greater value may be the use of CWRs as a source for valuable quantitative trait locus (QTL) variation. Zamir and his students and colleagues were among the first to propose and demonstrate a practical approach to utilizing the potential of CWRs as sources of important quantitative variation (Zamir 2008). Prior to this time, CWRs were primarily considered as sources of valuable qualitative genetic variants, particularly for traits such as disease resistance. Traits like yield and productivity were considered mainly in the context of cultivated genetic backgrounds. But an important insight offered by Zamir and colleagues focused on the observation that bottlenecks caused by domestication and modern breeding may have left behind valuable quantitative traits. By going back to CWRs, some of these valuable quantitative...