Genomic innovation for crop improvement

Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genomes and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access the large and complex genomes of crops and their wild relatives. These have helped to identify a wide spectrum of genetic variation and permitted the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems

Review on Concept and Impact of Double Haploid Techniques in Crop Improvement

Based on previous studies this review presents about double haploid technology and its role in crop improvement. Double haploids are plants those carry two sets of chromosomes that are created from the haploid plants. Different methods such as androgenesis (microspore or anther), gynogenesis (ovule or ovary) haploid inducer lines and wide crosses are used for developing haploid thereby double haploid. Though various chromosome doubling   agents found, colchicine has been widely using.  The successes of double haploid production relay on different factors like flower parts development stage, culture media, genotype, donor parent growth condition and haploid detection methods. This technology able shortens breeding cycle or time, complete genetic purity, efficient in genetic study, marker development, mutation and transformation better than traditional way of breeding. Generally, understanding DH technology has important contribution in accelerating breeding program for immediate reaction towards out breaking biotic and abiotic constraints and competitive to world market. Keywords: double haploid, haploid, crop improvemen

The evolutionary history of wild, domesticated, and feral brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions

Genetic architecture of wheat yield responses to drought

Maintaining wheat grain yield under expected more frequent and maybe severe drought episodes requires identifying the drought tolerance traits as well as deciphering the genetic basis of these traits responses to drought, and utilising potential symbiotic endophytes to alleviate drought effects. The aim of this project was to conduct an in-depth study of the genetic architecture of wheat responses to drought, deciphering the genetic basis of both source and sink traits under field conditions, as well as, investigating the ability of the endophyte fungus Piriformospora indica to increase yield in both well-watered and drought conditions and identify QTL underpinning drought-resistance traits influenced by endophytic growth. In the field trial, a representative subset of the elite eight-founder population, comprising 384 RILs, the founders and a check variety 'Kielder' were tested in rainfed vs irrigated field blocks, monitoring soil moisture content at different depth intervals. Field plots were phenotyped throughout the growing season using integrative drone-based and proximal sensing approaches. The results showed maximum soil moisture deficit (SMD) peaking over 120 mm in the rain fed plots, with large deficits (>75 mm) from late April that coincided with tillering and more prolonged large deficits from mid-June to mid-July(> I 00 mm), significantly decreasing crop canopy indices at all measured dates post-irrigation and causing significant increase in canopy temperature of rainfed plots, all driving an average yield reduction of 32.8% which was significantly genotype dependent. Also identifying traits most significantly (p:S0.00 I ) correlated with yield revealed grains.m-2 (r=0.68) and (r=0.72) and canopy temperature depression (CTD) (r=0.52) and (r=0.61) in rainfed and irrigated condition, respectively. QTL analysis for yield revealed a total of 16 novel QTL expressed commonly across both treatments explaining individually I to 4.5% as well as treatment dependent QTL. With remarkable examples of grain yield QTL collocating with major QTL such as grains.m-2 QTL on chromosome 3A and Rht-Dl pleiotropic region on chromosome 40 and highlighting significant SNP-SNP epistatic interactions for yield occasionally coinciding with QTL for crop canopy indices. Investigating the response of 200 MAGIC lines to P. indica inoculation showed the potential of the endophyte to significantly increase yield in well-watered and drought conditions, however, for most traits, there was significant difference in genotypes responses to colonization. Several QTL unique to colonized plants were detected on most chromosomes and linked to measured traits under drought, Those QTL can be investigated as candidate genes governing the symbiosis between wheat and P. indica

The evolutionary history of wild, domesticated, and feral Brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions

Advancing genomics to enable anticipatory breeding of resistance in Brassica crops to diseases of global importance

White rust (WR) (caused by the oomycete Albugo candida) inflicts significant yield decline in brassica crops across the world. It is a particular problem in countries like India, where resource poor farmers cultivating oilseed mustard (Brassica juncea) suffer between 30-60% yield losses per year. Breeding for host resistance is the most effective and environmentally friendly way of protecting brassica crops from WR. Rapid evolution of the pathogen highlights the need to efficiently map multiple resistance genes for combined integration into cultivars. Here we present novel methods for achieving this, with an emphasis on directly mapping from undeveloped genebank populations. In this work, the application of Whole Genome Resequencing (WGS) and Bulked Segregant Analysis (BSA) proved to be highly effective for rapidly mapping sixteen major effect white rust resistance (WRR) QTLs across five geographically diverse Brassica rapa genebank populations, including a landrace and a wild species. This includes a QTL mapped on chromosome 6, containing a WRR allele that provides resistance to Donskaja-virulent UK race 2 isolate AcBjDC. WGS for all QTLs has been scrutinised, allowing identification of various polymorphic candidate WRR genes. WRR was also explored in the Brassica oleracea EBH527 x A12DH mapping population, where a previously fine-mapped ACA2 locus contains a recessive race non-specific resistance. A CRISPR-Cas9 knockout of the primary candidate (a GDSL Lipase) yielded no alteration to susceptibility and WGS of the two parents has since been used to identify other potentially causal mutations within the region. WGS-BSA was also applied here to map a dominant resistance locus in tight-linkage to ACA2 from segregating recombinant line EH177. Finally, Oxford Nanopore Technology long-read sequencing was used to produce high-quality genome assemblies for race 2 isolates AcBj12 and AcBjDC, augmented with Illumina reads. The AcBj12_ONT assembly provided a 30 % improvement in contiguity relative to previous efforts using PacBio data. Comparative genomics that included Donskaja-virulent isolate Ac2v was used to document allelic variation in “CCG” class effectors that provides a platform for future identification of the Avr elicitor. Collectively, methods presented here enhance rapid identification of loci and candidate genes for the benefit of global brassica production

Genetic Analysis of a Non-Germinating Mutant of Arabidopsis Thaliana

Seed germination is partially controlled by plant hormone gibberellins (GAs). Chemical mutagenesis yielded an Arabidopsis thaliana mutant gm11, which has an absolute gibberellin requirement for seed germination. This mutant exhibited phenotypes of GA-rescuable dwarfs, including dark-green leaves, and reduced fertility. However, with repeated GA treatment, gm11 develops into fertile plants with a nearly wild type phenotype. Bulked-segregant analysis mapped gm11 to the bottom arm of chromosome 1, and subsequent next-generation mapping revealed that the mutation is a G → A transition in At1g79460 (GA2), creating a premature stop codon. This gene encodes an ent-kaurene synthase (KS) which catalyzes the conversion of copalyl diphosphate to ent-kaurene in the GA biosynthesis pathway. Further genetic analysis suggests that gm11 is allelic to ga2 and has been named ga2-11. This work demonstrated a genetic finding useful for further understanding the molecular process underlying dormancy and germination

Translational Genomics for Crop Breeding: Biotic Stress, Volume 1

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 essential reference for crop scientists, geneticists, breeders, industry personnel and advanced students in the field

Metabolomics-Driven Mining of Metabolite Resources:Applications and Prospects for Improving Vegetable Crops

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants

Molecular Genetics, Genomics and Biotechnology of Crop Plants Breeding

This Special Issue on molecular genetics, genomics, and biotechnology in crop plant breeding seeks to encourage the use of the tools currently available. It features nine research papers that address quality traits, grain yield, and mutations by exploring cytoplasmic male sterility, the delicate control of flowering in rice, the removal of anti-nutritional factors, the use and development of new technologies for non-model species marker technology, site-directed mutagenesis and GMO regulation, genomics selection and genome-wide association studies, how to cope with abiotic stress, and an exploration of fruit trees adapted to harsh environments for breeding purposes. A further four papers review the genetics of pre-harvest spouting, readiness for climate-smart crop development, genomic selection in the breeding of cereal crops, and the large numbers of mutants in straw lignin biosynthesis and deposition