Chengdao Li

Artificial Intelligence (AI) has emerged as a key driver of precision agriculture, facilitating enhanced crop productivity, optimized resource management, and sustainable farming practices. Also, the expansion of genome sequencing technology has greatly increased crop genomic resources, offering deeper insights into genetic variation and enhancing desirable crop traits for better performance across various environments. Machine learning (ML) and deep learning (DL) algorithms are gaining traction for genotype-to-phenotype prediction, due to their excellence in capturing complex interactions within large, high-dimensional datasets. In this work, we present a new LSTM autoencoder-based model for barley genotype-to-phenotype prediction, specifically targeting flowering time and grain yield estimation. Our model outperformed the other baseline methods, highlighting its effectiveness in handling complex, high-dimensional agricultural datasets and enhancing the accuracy of crop phenotype prediction predictions. This approach has the potential to optimize crop yields and improve management practices.

The growing global human population requires improvement in crop production to meet food demand. Crop improvement via breeding can sustainably increase yield production and stability and decrease dependence on fertilisers and pesticides. Recent progresses in pangenomics and machine learning provide opportunities for crop improvement. The development of long-read sequencing technologies is helping overcome challenges in crop genome assembly caused by highly repeated regions or heterozygous sequences. As a result, high-quality crop reference genomes and pangenomes are becoming increasingly accessible, enhancing downstream analyses such as variant discovery and association mapping, which are crucial for identifying breeding targets for crop improvement. Machine learning approaches help to characterise the growing volume of plant genomic data and facilitating real-time high-throughput phenotyping of agronomic traits. Moreover, crop databases that integrate the increasing amount of genotypes identified using pangenomes and machine learning approaches are valuable for uncovering novel trait-associated candidate genes. With an increasing understanding of crop genetics, genomic selection and genome editing emerge as powerful tools for cultivating crops that are resistant to both biotic and abiotic stresses, while also achieving high productivity.

This chapter reviews genetic diversity in barley and its role in improving varieties, including adaptation to abiotic stresses. Sulphur is an essential macronutrient required in plants for normal growth and development. Its deficiency in agricultural soils reduces grain yield and grain quality traits. Studies conducted with barley and wheat varieties demonstrate substantial variations among crops and varieties in their response to application of different levels of sulphur. The chapter looks at factors affecting sulphur nutrition in barley and the potential role of genetic differences in breeding more resilient varieties.

Frost is an important stress factor both at vegetative and reproductive stages of barley. Frost, otherwise known as low temperature stress, damages leaf and stem, causes floret sterility, increases screenings, and reduces grain yield and germination causing substantial loses. To curb these problems, numerous studies have been undertaken elsewhere on frost tolerance in barley both at vegetative and reproductive stages. These studies used field or controlled environments, or a combination of field and controlled environments to understand response of barley genotypes to frost. At the vegetative stage, percentage survival, electrolyte leakage, ABA content, cold induced protein contents, and molecular markers as diagnostic tools have been used to distinguish between barley cultivars for frost tolerance. Reproductive stage traits used to distinguish between barley genotypes for frost tolerance include floret sterility, grain damage, and grain yield and associated molecular markers. Measurement for frost tolerance at reproductive stages has been reported to be complex. Despite substantial research efforts to understand frost tolerance in barley, improvement for this stress at the reproductive stage of development remains challenging. This is in contrast to vegetative stage frost tolerance in winter barleys that not only tolerate but also require low temperature to transit from the vegetative stage to the reproductive stage. Recent developments in barley genomics may help to exploit high genotypic variation in barley for frost tolerance at the reproductive stage. Frost tolerance genes already mapped on various chromosomes would play key roles in improving commercial barley varieties for reproductive stage frost tolerance. This chapter is an overview of barley genotypic variation, methods used in frost tolerance studies, and genetic factors reported elsewhere to be associated with frost tolerance.

Research reports show high genetic diversity in exotic germplasm, which include landraces and wild barley, and low genetic diversity in commercial cultivars. However, exotic germplasm have been reported to be underutilized in barley cultivar development. This is probably due to consumer demand on high yield and high-quality barley cultivars especially for malting purposes, and poor agronomic and quality traits in exotic germplasm. Nevertheless, exotic germplasm have genes that can help reduce the damage caused by biotic and abiotic stress factors. Mass screening and evaluation helped to identify important genotypes that contributed to the development of commercial cultivars. To increase the efficiency of identifying genotypes with important genes from barley germplasm conserved ex situ worldwide, systematic approaches need to be used. The Core-Collection concept, based on agromorphologic traits, and the Focused Identification of Germplasm Strategy (FIGS), based on ecological data of collection site matched with the ecology of the stress factors, can play useful roles. Although such approaches can substantially reduce the number of germplasm for evaluation, they have their own shortcomings that may limit their uses.

Exploration and utilization of new germplasm has played a pivotal role for the increase of barley yield and improvement of malting quality in the last century. The denso gene from Triumph, ari-GP gene from Golden Promise, and uze gene from the Southeast Asian barley have become the cornerstones for modern barley breeding success in the world. Recently, success for deployment of the acid soil and boron toxicity tolerance genes in the Australian barley varieties have further demonstrated the high value of new germplasm for enhancing barley productivity and sustainability. The consumption of barley keeps increasing with the growing population and the improvements in standards of living around the world. Barley is mainly used as raw material for feed and beer production. In recent years, use of barley as a functional food has been intensified due to its special chemical components, which are beneficial to human health. In this book, we present the advances in exploitation and utilization of barley germplasm for food and malt barley improvement. As a cereal crop, barley is often grown in the marginal soils. Climate irregularity has added new challenges arley production. Understanding the mechanisms for barley’s environmental stress tolerance is essential for future barley production. This book focuses on recent advances in barley abiotic stress tolerance, including drought, salinity, acidic soil (aluminum toxicity), waterlogging, and frost, with an emphasis on novel germplasm and technologies for germplasm exploration. The international community is still in the early stages of completing the barley genome sequence. However, recent advances in sequencing technology will have a dramatic impact on barley germplasm exploration and utilization. Thus, this book also includes one chapter on sequencing technologies and their potential applications. The authors for each of the chapters in this book are researchers who are on the frontier in their specific research areas. We aim to cover the most recent advances for barley quality and abiotic stress tolerance, with an emphasis on practical implementation. The book will provide a good reference both for barley genetics and breeding research. This book can be read as a companion to Genetic Improvement of Barley Malt Quality. The malting quality chapter in this book is a supplementary of the previous book with emphasis on the Canadian barley germplasm for malting quality improvement, as Canadian barley has been the international benchmark for malting quality. Australia is the world’s largest malting barley exporter and China is the largest malting barley importer. This interrelationship has fostered the two nations’ long-term collaboration on barley abiotic stress tolerance. Many of the authors of this book have worked on these collaborative projects. Thus, this book can be seen as a summary of the collaborative research projects of the two countries. In this regard, we would like to acknowledge the support from the Australian Grain Research and Development Corporation and the Natural Science Foundation of China.

The release of barley genome sequences will accelerate the genomic and genetic research in barley. Using next-generation sequencing (NGS) technology, it is possible to re-sequence entire barley genomes or transcriptomes more efficiently and economically than ever before. The chapter covers barley genetic and physical maps, and barley genome sequences. We summarized NGS sequencing technologies and their applications in genetic marker development, QTL mapping, gene cloning, transcript profiling identification, and epigenetic mechanism discovery in barley. These technologies will provide efficient tools to explore barley germplasm and improve breeding efficiency.

Excess of water affects plant growth and metabolism dramatically. Limited oxygen availability and changes in soil redox potential and pH result in energy shortage, nutritional disturbances, phytotoxicity, and oxidative injury to plants. This chapter reviews basic mechanisms exploited by plants to combat these damages. This includes constitutive or stress-induced aerenchyma development, adventitious root formation, changes to metabolic profile and energy use strategies, changes in antioxidant pool, and increased tolerance to elemental and organic phytotoxins. We also discuss signal transduction pathway mediating plant adaptive responses to waterlogging, with the main emphasis on Sub1 gene cluster. We then discuss the recent progresses in the quantitative traits locus (QTL) mapping for some key traits associated with waterlogging and submerging stress tolerance, how the combined network of hormones and metabolites is involved in regulation of plant adaptive responses to waterlogging, and how this knowledge should guide the breeding of tolerant varieties or developing novel sources of waterlogging-tolerant crops are also illustrated. Finally, we discuss methods to explore and develop waterlogging tolerant genotypes.

Narrowing genetic basis is the bottleneck for modern plant improvement. Genetic variation in wild barley Hordeum spontaneum is much greater than that of either cultivated or landrace H. vulgare gene pool. It represents a valuable but underutilised gene pool for barley improvement as no biological isolation barriers exist between H. spontaneum and cultivated barley. Novel sources of new genes were identified from H. spontaneum for yield, quality, disease resistance and abiotic tolerance. Quantitative trait loci (QTLs) were mapped to all barley chromosomes. A QTL on chromosome 4H from the wild barley consistently increased yield by 7.7% across six test environments. Wild barley H. spontaneum was demonstrated as key genetic resource for drought and salinity tolerance. Two QTLs on chromosomes 2H and 5H increased grain yield by 12–22% under drought conditions. Several QTL clusters were present on chromosomes 1H, 2H, 4H, 6H and 7H from H. spontaneum for drought and salinity tolerance. Numerous candidate genes were identified to associate with tolerance to drought or salinity, and some of the candidate genes co-located with the QTLs for drought tolerance. QTLs/genes for resistance to powdery mildew, leaf rust and scald were mapped to all chromosomes. Scald resistance was found in at least five chromosome locations (1HS, 3H, 6HS, 7HL and 7HS) from H. spontaneum, and simple molecular markers were developed to accelerate transferring of these genes into cultivated barley. Novel beta-amylase allele from H. spontaneum was used to improve barley malting quality. Advanced backcross QTL provides an efficiency approach to transfer novel genes from H. spontaneum to cultivated barley.