Translational Genomics for Crop Breeding, Volume 1

Biotic Stress

Rajeev Varshney, Roberto Tuberosa

• Publisher: Wiley-Blackwell
• Year: 2013
• ISBN:
  9781118728321
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

Genomic Applications for Crop Breeding: Biotic Stress is the first of two volumes looking at the latest advances in genomic applications to crop breeding. This volume focuses on genomic-assisted advances for improving economically important crops against biotic stressors, such as viruses, fungi, nematodes, and bacteria. Looking at key advances in crops such as rice, barley, wheat, and potato amongst others, Genomic Applications for Crop Breeding: Biotic Stress will be an essentialreference for crop scientists, geneticists, breeders, industry personnel and advanced students in the field.

Chapter 1

Translational Genomics in Crop Breeding for Biotic Stress Resistance: An Introduction

Rajeev K. Varshney and Roberto Tuberosa

Abstract

Biotic stresses pose a major threat to crop productivity. Crops are challenged by a plethora of biotic stresses, but only a limited number of key pests and diseases cause the vast majority of economic losses in a particular crop. Plant protection measures such as application of pesticides and deployment of resistant gene(s)/quantitative trait loci (QTLs) into cultivars have so far been quite successful in curtailing the losses; however, these measures have also led to the constant evolution of new biotypes/pathotypes/strains/races of pest and disease organisms. Hence, there is a continuous need to identify genomic regions that can impart resistance against these variants. The availability of large-scale genomic resources in many crop species has enhanced our understanding on the path to developing host-plant resistance. As a result, numerous race-specific gene(s) and QTLs have now been identified and cloned with the help of molecular markers. It is quite exciting that these genomic regions are being introgressed into breeding programs of many crops. The objective of this book is to critically review the current availability and utilization of genomic tools for major biotic stresses in important cereals, legumes, vegetables, and tuber and oilseed crop. The book also summarizes the success stories achieved through application of genomics-assisted breeding (GAB), as well as the scope for deployment of modern breeding methods such as marker-assisted backcrossing (MABC) and genomic selection in the era of next-generation sequencing (NGS) technologies, which have the potential to advance the genetic gains for enhancing resilience against biotic stress. This chapter summarizes highlights of different chapters included in the book that is expected to be a resource for young researchers, GAB practitioners, and policy makers for employing better strategies toward achieving food security.

Introduction

Several biotic and abiotic stresses challenge crop productivity. Breeders try to develop superior lines by making crosses and selecting the best lines based on their agronomic performance, but the entire process is expensive and takes several years. During the past two decades, remarkable progress in the area of genomics and molecular genetics has greatly improved our basic understanding of resistance to biotic stresses and tolerance of abiotic stresses. Genomics approaches can enhance the precision and efficiency of breeding programs through a better prediction of phenotype from a given genotype – process generally referred to as genomics-assisted breeding (GAB) (Varshney et al. 2005).

Among different GAB approaches, the marker-assisted backcrossing (MABC) approach has been quite successful in transferring the target genomic regions in elite cultivars (Varshney et al. 2012). MABC for gene pyramiding coupled with selection for the genetic background of the recurrent parent and recombination at the target region(s) could lead to faster and better product delivery, thereby increasing productivity and improving livelihoods of the smallholder farmers (Collard et al. 2008).

Biotic stress caused by pests and diseases continues to pose a significant risk to crop productivity in spite of years of investments in research and development aimed at understanding host-plant interaction and finding more effective methods to control it (Lucas 2011). It has been estimated that even after the deployment of pesticides and improved cultivars in the target environment with resistance to biotic stresses, yield losses resulting from pests and diseases can still reach 20-30% (Oerke 2006). This loss may be attributed to the constant and rapid evolution of new virulent pathogens/pests such as Ug99 for wheat stem rust (Levine and D'Antonio 2003), as well as to their spread to new regions in response to climate change and the adoption of different agricultural practices (e.g., minimum tillage).

Abiotic stresses, such as drought, salinity, cold, submergence, mineral toxicity, and others, also hamper growth, yield, and yield quality of crop plants. In fact, these abiotic stresses represent the main cause of crop failure worldwide, reducing average yields for major crops by more than 50%. Overall, as compared to biotic stresses, abiotic stresses pose more serious constraints to crop production, particularly in view of rapidly deteriorating environmental conditions. Quality traits are the other important class of target traits that breeders select for in order to improve crop productivity as well as nutritional quality.

In recent years, large-scale genomic resources have been developed and are being utilized in breeding programs for several crop species (Varshney et al. 2009; Tuberosa et al. 2011). These advances in genomics research have greatly contributed to the conversion of so-called orphan crops to genomic resources-rich crops (Varshney et al. 2009, 2010) and to the enhanced precision and speed of breeding programs. In several cases, GAB has delivered superior lines that have been used for developing new varieties or hybrids (Simpson et al. 2003; Sundaram et al. 2008; Ceballos et al. 2012; Singh et al. 2012). However, introgression of QTLs has not always been successful in crop breeding, and even less so for the improvement of tolerance to abiotic stresses (Collins et al. 2008). Therefore, GAB practices have also offered some lessons to the molecular breeding practitioners.

In view of the above, the two volumes on Translational Genomics for Crop Breeding compile a number of manuscripts that report on success stories either completed or still in progress, as well as the lessons learned from GAB work on different crops. Volume I compiles 16 chapters that review the current status and recent advances in the application of GAB approaches for biotic stress resistance. Volume II is a compendium of 13 chapters on GAB for enhancing abiotic stress tolerance and improving crop quality.

This introductory chapter of Volume I provides key highlights of GAB applications to enhance biotic stress tolerance. Since the majority (estimated to be ca. 60-70%) of our major caloric intake is obtained directly or indirectly from cereals, the first five chapters summarize the progress on the improvement of biotic stress tolerance in five major cereals, namely rice, maize, wheat, barley, and sorghum. The contribution of legumes to enhancing nutrition in the daily diet has been largely recognized apart from their well-known ability for nitrogen-fixation. The next five chapters deal with GAB applications for important biotic stresses in legumes, namely soybean, peanut, common bean, cowpea, and chickpea. Two additional chapters deal with GAB for enhancing the tolerance of potato and tomato to late blight, one of the most devastating diseases of these two important vegetable crops. The three final chapters highlight GAB efforts toward improving disease resistance in lettuce, cassava, and Brassica species.

Improving Disease Resistance in Cereals

Bacterial blight (BB), effected by Xanthomonas oryzae pv. oryzae (Xoo), is a major constraint for rice production, with reported yield losses of up to 50% (Ou 1985). Recently several genes and QTLs have been identified for various virulent strains. Chapter 2 by Kou and Wang provides a comprehensive review of and valuable insights to understanding the interaction between rice and Xoo pathogen. This review provides strategies and prior knowledge for effective deployment of resistance genes in target environment against Xoo pathogen. Until now, more than 35 BB rice resistance genes have been identified and 7 of these have been isolated. MABC has been quite successful in the case of BB, and various genes such as Xa4, xa5, Xa7, xa13, Xa21, Xa23 in single or in pyramided form have been introgressed in popular varieties/parental lines such as, Samba Mahsuri, Pusa Basmati 1, Minghui 63, and have been developed and released in India and China (Gopalakrishnan et al. 2008; Sundaram et al. 2008; Perumalsamy et al. 2010; Huang et al. 2012; Singh et al. 2012).

Chapter 3 by Jamann, Nelson, and Balint-Kurti provides a comprehensive survey of the genetic basis of disease resistance in maize, especially against fungal diseases. In the past, bi-parental linkage mapping was commonly adopted for mapping important genes and QTLs. However, in recent years, modern mapping approaches such as nested association mapping (NAM), which is an effective combination of linkage and linkage-disequilibrium approaches, are becoming increasingly popular (Yu et al. 2008). The chapter reports on the use of the NAM approach to identify genomic regions responsible for three important diseases in maize, namely southern leaf blight, northern leaf blight, and gray leaf spot (Benson et al. 2011; Kump et al. 2011; Poland et al. 2011). In addition, the authors outline the potential of genomic selection to accelerate the breeding efforts for disease resistance, especially in cases where small-effect and environment-sensitive QTLs are involved, as in Aspergillus ear rot and aflatoxin accumulation (Warburton et al. 2009). These genetic studies provide an insight into the disease resistance mechanism, thereby helping molecular breeders understand the genes to be used for their deployment in elite cultivars.

In the case of wheat, among several other diseases, Fusarium head blight (FHB) is an age-old and severe one (Leonard and Bushnell 2003). Importantly, contamination caused by fusarium secondary metabolites, known as mycotoxins, poses a major threat to animal and human health (Van Egmond 2004). Extensive QTL studies for FHB resistance have led to the identification of 19 meta-QTLs spread across wheat chromosomes (Buerstmayr et al. 2009; Liu et al. 2009; Löffler et al. 2009). These GAB efforts for FHB have been summarized in Chapter 4 by Hermann Buerstmayr, Maria Buerstmayr, and Schweiger and Steiner. A closely linked codominant marker is always a prerequisite for making any MABC program a success. In particular, Umn10, a PCR-based marker linked to a major gene (Fhb1) located on the long arm of chromosome 3B and explaining 40-50% of phenotypic variance (Rosyara et al. 2009), is being used routinely in breeding programs of both hexaploid and tetraploid wheat.

In barley, improving virus resistance is one of the top research priorities because it has a serious impact on its production, particularly in Western Europe. Much work has been done in the recent past toward identification of resistance genes for four major viruses affecting barley (Ordon et al. 2009). As a result, molecular markers are now available for fast introgression. In a recent study, improved DH-lines have been developed for Barley Yellow Dwarf Virus through markers (Riedel et al. 2011). Chapter 5 by Ordon and Perovic covers recent advances toward development of genomic tools for transferring virus resistance into elite cultivars via GAB. The authors also highlight the importance and use of allele mining and utilization of high-throughput SNP technologies for carrying out precision breeding activities in barley.

In sorghum, Striga is the most damaging obligate parasite pest that leads to yield loss of up to 90% (Ejeta 2007). It is particularly severe in East Africa and some regions in the United States and Asia. Although much progress has been made toward QTL analysis and Marker-assisted selection (MAS) for improving resistance to Striga, the molecular mechanisms behind the establishment of parasitism are still not well understood. In Chapter 6, Deshpande, Mohamed, and Hash describe several aspects for elucidating the molecular mechanisms of Striga resistance through development of bioassays, exploring the pathway, and identifying the stages as entry points for breeding resistance to Striga, as well as GAB approaches to developing sorghum lines with enhanced resistance to Striga. The authors also discuss the utility of next-generation sequencing (NGS) technologies for identifying the functional basis of Striga resistance.

Improving Disease Resistance in Legumes

Among different legumes, soybean, known for its edible oil and protein content, is an important industry crop. North America and South America are the major production areas, accounting for nearly 86% of total soybean production worldwide (http://www.soysta...

Table of contents

• Cover
• Title Page
• Copyright
• Foreword
• Preface
• Chapter 1: Translational Genomics in Crop Breeding for Biotic Stress Resistance: An Introduction
• Chapter 2: Bacterial Blight Resistance in Rice
• Chapter 3: The Genetic Basis of Disease Resistance in Maize
• Chapter 4: Genomics-Assisted Breeding for Fusarium Head Blight Resistance in Wheat
• Chapter 5: Virus Resistance in Barley
• Chapter 6: Molecular Breeding for Striga Resistance in Sorghum
• Chapter 7: Nematode Resistance in Soybean
• Chapter 8: Marker-Assisted Selection for Biotic Stress Resistance in Peanut
• Chapter 9: Organization of Genes Conferring Resistance to Anthracnose in Common Bean
• Chapter 10: Enabling Tools for Modern Breeding of Cowpea for Biotic Stress Resistance
• Chapter 11: Disease Resistance in Chickpea
• Chapter 12: Resistance to Late Blight in Potato
• Chapter 13: Late Blight of Tomato
• Chapter 14: Marker-Assisted Selection for Disease Resistance in Lettuce
• Chapter 15: Marker-Assisted Breeding for Cassava Mosaic Disease Resistance
• Chapter 16: Genetics and Gene Mapping of Disease Resistance in Brassica
• Appendix I – Contributors
• Appendix II – Reviewers
• Index