Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America.

Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world's largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases.

Highly divergent satellitomes of two barley species of agronomic importance, Hordeum chilense and H. vulgare.

In this paper, we have performed an in-depth study of the complete set of the satellite DNA (satDNA) families (i.e. the satellitomes) in the genome of two barley species of agronomic value in a breeding framework, H. chilense (H1 and H7 accessions) and H. vulgare (H106 accession), which can be useful tools for studying chromosome associations during meiosis. The study has led to the analysis of a total of 18 satDNA families in H. vulgare, 25 satDNA families in H. chilense (accession H1) and 27 satDNA families in H. chilense (accession H7) that constitute 46 different satDNA families forming 36 homology groups. Our study highlights different important contributions of evolutionary and applied interests. Thus, both barley species show very divergent satDNA profiles, which could be partly explained by the differential effects of domestication versus wildlife. Divergence derives from the differential amplification of different common ancestral satellites and the emergence of new satellites in H. chilense, usually from pre-existing ones but also random sequences. There are also differences between the two H. chilense accessions, which support genetically distinct groups. The fluorescence in situ hybridization (FISH) patterns of some satDNAs yield distinctive genetic markers for the identification of specific H. chilense or H. vulgare chromosomes. Some of the satellites have peculiar structures or are related to transposable elements which provide information about their origin and expansion. Among these, we discuss the existence of different (peri)centromeric satellites that supply this region with some plasticity important for centromere evolution. These peri(centromeric) satDNAs and the set of subtelomeric satDNAs (a total of 38 different families) are analyzed in the framework of breeding as the high diversity found in the subtelomeric regions might support their putative implication in chromosome recognition and pairing during meiosis, a key point in the production of addition/substitution lines and hybrids.

Genetic resources of African mahogany in Brazil: genomic diversity and structure of forest plantations.

BACKGROUND: African mahogany species (Khaya sp.) have been introduced to Brazil gaining increasing economic interest over the last years, as they produce high quality wood for industrial applications. To this date, however, the knowledge available on the genetic basis of African mahogany plantations in Brazil is limited, which has driven this study to examine the extent of genetic diversity and structure of three cultivated species (Khaya grandifoliola, Khaya senegalensis and Khaya ivorensis) and their prospects for forest breeding. RESULTS: In total, 115 individuals were genotyped (48 of K. grandifoliola, 34 of K. senegalensis and 33 of K. ivorensis) for 3,330 filtered neutral loci obtained from genotyping-by-sequencing for the three species. The number of SNPs varied from 2,951 in K. ivorensis to 4,754 in K. senegalensis. Multiloci clustering, principal component analysis, Bayesian structure and network analyses showed a clear genetic separation among the three species. Structure analysis also showed internal structure within each species, highlighting genetic subgroups that could be sampled for selecting distinct genotypes for further breeding, although the genetic distances are moderate to low. CONCLUSION: In our study, SNP markers efficiently assessed the genomic diversity of African mahogany forest plantations in Brazil. Our genetic data clearly separated the three Khaya species. Moreover, pairwise estimates of genetic distances among individuals within each species showed considerable genetic divergence among individuals. By genotyping 115 pre-selected individuals with desirable growth traits, allowed us not only to recommend superior genotypes but also to identify genetically distinct individuals for use in breeding crosses.

In silico analysis of Apostasia wallichii (Apostasioideae) and Ludisia discolor (Orchidoideae) orchids reveals different repeats composition despite the same genome size.

Repetitive sequences can lead to variation in DNA quantity and composition among species. The Orchidaceae, the largest angiosperm family, is divided into five subfamilies, with Apostasioideae as the basal group and Orchidoideae and Epidendroideae showing high diversification rates. Despite their different evolutionary paths, some species in these groups have similar nuclear DNA content. This study focuses on one example to understand the dynamics of major repetitive DNAs in the nucleus. We used Next-Generation Sequencing (NGS) data from Apostasia wallichii (Apostasioideae) and Ludisia discolor (Orchidoideae) to identify and quantify the most abundant repeats. The repetitive fraction varied in abundance (27.5% in L. discolor and 60.6% in A. wallichii) and composition, with LTR retrotransposons of different lineages being the most abundant repeats in each species. Satellite DNAs showed varying organization and abundance. Despite the unbalanced ratio between single-copy and repetitive DNA sequences, the two species had the same genome size, possibly due to the elimination of non-essential genes. This phenomenon has been observed in other Apostasia and likely led to the proliferation of transposable elements in A. wallichii. Deep genome information in the future will aid in understanding the contraction/expansion of gene families and the evolution of sequences in these genomes.

A Penalized Regression Method for Genomic Prediction Reduces Mismatch between Training and Testing Sets.

Genomic selection (GS) is changing plant breeding by significantly reducing the resources needed for phenotyping. However, its accuracy can be compromised by mismatches between training and testing sets, which impact efficiency when the predictive model does not adequately reflect the genetic and environmental conditions of the target population. To address this challenge, this study introduces a straightforward method using binary-Lasso regression to estimate ß coefficients. In this approach, the response variable assigns 1 to testing set inputs and 0 to training set inputs. Subsequently, Lasso, Ridge, and Elastic Net regression models use the inverse of these ß coefficients (in absolute values) as weights during training (WLasso, WRidge, and WElastic Net). This weighting method gives less importance to features that discriminate more between training and testing sets. The effectiveness of this method is evaluated across six datasets, demonstrating consistent improvements in terms of the normalized root mean square error. Importantly, the model's implementation is facilitated using the glmnet library, which supports straightforward integration for weighting ß coefficients.

Genome-Wide Identification of a Maize Chitinase Gene Family and the Induction of Its Expression by Fusarium verticillioides (Sacc.) Nirenberg (1976) Infection.

Maize chitinases are involved in chitin hydrolysis. Chitinases are distributed across various organisms including animals, plants, and fungi and are grouped into different glycosyl hydrolase families and classes, depending on protein structure. However, many chitinase functions and their interactions with other plant proteins remain unknown. The economic importance of maize (Zea mays L.) makes it relevant for studying the function of plant chitinases and their biological roles. This work aims to identify chitinase genes in the maize genome to study their gene structure, family/class classification, cis-related elements, and gene expression under biotic stress, such as Fusarium verticillioides infection. Thirty-nine chitinase genes were identified and found to be distributed in three glycosyl hydrolase (GH) families (18, 19 and 20). Likewise, the conserved domains and motifs were identified in each GH family member. The identified cis-regulatory elements are involved in plant development, hormone response, defense, and abiotic stress response. Chitinase protein-interaction network analysis predicted that they interact mainly with cell wall proteins. qRT-PCR analysis confirmed in silico data showing that ten different maize chitinase genes are induced in the presence of F. verticillioides, and that they could have several roles in pathogen infection depending on chitinase structure and cell wall localization.

Chromosome-scale genome assembly and annotation of Paspalum notatum Flüggé var. saurae.

Paspalum notatum Flüggé is an economically important subtropical fodder grass that is widely used in the Americas. Here, we report a new chromosome-scale genome assembly and annotation of a diploid biotype collected in the center of origin of the species. Using Oxford Nanopore long reads, we generated a 557.81 Mb genome assembly (N50 = 56.1 Mb) with high gene completeness (BUSCO = 98.73%). Genome annotation identified 320 Mb (57.86%) of repetitive elements and 45,074 gene models, of which 36,079 have a high level of confidence. Further characterisation included the identification of 59 miRNA precursors together with their putative targets. The present work provides a comprehensive genomic resource for P. notatum improvement and a reference frame for functional and evolutionary research within the genus.

De novo domestication in the Solanaceae: advances and challenges.

The advent of highly efficient genome editing (GE) tools, coupled with high-throughput genome sequencing, has paved the way for the accelerated domestication of crop wild relatives. New crops could thus be rapidly created that are well adapted to cope with drought, flooding, soil salinity, or insect damage. De novo domestication avoids the complexity of transferring polygenic stress resistance from wild species to crops. Instead, new crops can be created by manipulating major genes in stress-resistant wild species. However, the genetic basis of certain relevant domestication-related traits often involve epistasis and pleiotropy. Furthermore, pan-genome analyses show that structural variation driving gene expression changes has been selected during domestication. A growing body of work suggests that the Solanaceae family, which includes crop species such as tomatoes, potatoes, eggplants, peppers, and tobacco, is a suitable model group to dissect these phenomena and operate changes in wild relatives to improve agronomic traits rapidly with GE. We briefly discuss the prospects of this exciting novel field in the interface between fundamental and applied plant biology and its potential impact in the coming years.

Non-B DNA in plant genomes: prediction, mapping, and emerging roles.

Regulating gene expression in plant development and environmental responses is vital for mitigating the effects of climate change on crop growth and productivity. The eukaryotic genome largely shows the canonical B-DNA structure that is organized into nucleosomes with histone modifications shaping the epigenome. Nuclear proteins and RNA interactions influence chromatin conformations and dynamically modulate gene activity. Non-B DNA conformations and their transitions introduce novel aspects to gene expression modulation, particularly in response to environmental shifts. We explore the current understanding of non-B DNA structures in plant genomes, their interplay with epigenomics and gene expression, and advances in methods for their mapping and characterization. The exploration of so far uncharacterized non-B DNA structures remains an intriguing area in plant chromatin research and offers insights into their potential role in gene regulation.

Chromosome-scale genome assembly and annotation of the tetraploid potato cultivar Diacol Capiro adapted to the Andean region.

Potato (Solanum tuberosum) is an essential crop for food security and is ranked as the third most important crop worldwide for human consumption. The Diacol Capiro cultivar holds the dominant position in Colombian cultivation, primarily catering to the food processing industry. This highly heterozygous, autotetraploid cultivar belongs to the Andigenum group and it stands out for its adaptation to a wide variety of environments spanning altitudes from 1,800 to 3,200 meters above sea level. Here, a chromosome-scale assembly, referred to as DC, is presented for this cultivar. The assembly was generated by combining circular consensus sequencing with proximity ligation Hi-C for the scaffolding and represents 2.369 Gb with 48 pseudochromosomes covering 2,091 Gb and an anchor rate of 88.26%. The reference genome metrics, including an N50 of 50.5 Mb, a BUSCO (Benchmarking Universal Single-Copy Orthologue) score of 99.38%, and an Long Terminal Repeat Assembly Index score of 13.53, collectively signal the achieved high assembly quality. A comprehensive annotation yielded a total of 154,114 genes, and the associated BUSCO score of 95.78% for the annotated sequences attests to their completeness. The number of predicted NLR (Nucleotide-Binding and Leucine-Rich-Repeat genes) was 2107 with a large representation of NBARC (for nucleotide binding domain shared by Apaf-1, certain R gene products, and CED-4) containing domains (99.85%). Further comparative analysis of the proposed annotation-based assembly with high-quality known potato genomes, showed a similar genome metrics with differences in total gene numbers related to the ploidy status. The genome assembly and annotation of DC presented in this study represent a valuable asset for comprehending potato genetics. This resource aids in targeted breeding initiatives and contributes to the creation of enhanced, resilient, and more productive potato varieties, particularly beneficial for countries in Latin America.

Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses.

GDSL-type esterase/lipase protein (GELP) genes are crucial in the specialized lipid metabolism, in the responses to abiotic stresses, and in the regulation of plant homeostasis. R. communis is an important oilseed crop species that can sustain growth and productivity when exposed to harsh environmental conditions. Herein, we raised the question of whether the GELP gene family could be involved in the acquisition of R. communis tolerance to abiotic stresses during seed germination and seedling establishment. Thus, we used bioinformatics and transcriptomics to characterize the R. communis GELP gene family. R. communis genome possesses 96 GELP genes that were characterized by extensive bioinformatics, including phylogenetic analysis, subcellular localization, exon-intron distribution, the analysis of regulatory cis-elements, tandem duplication, and physicochemical properties. Transcriptomics indicated that numerous RcGELP genes are readily responsive to high-temperature and salt stresses and might be potential candidates for genome editing techniques to develop abiotic stress-tolerant crops.

Conservation genomics of the wild pumpkin Cucurbita radicans in Central Mexico: The influence of a changing environment on the genetic diversity and differentiation of a rare species.

The genetic diversity found in natural populations is the result of the evolutionary forces in response to historical and contemporary factors. The environmental characteristics and geological history of Mexico promoted the evolution and diversification of plant species, including wild relatives of crops such as the wild pumpkins (Cucurbita). Wild pumpkin species are found in a variety of habitats, evidencing their capability to adapt to different environments. Despite the potential value of wild Cucurbita as a genetic reservoir for crops, there is a lack of studies on their genetic diversity. Cucurbita radicans is an endangered species threatened by habitat destruction leading to low densities in small and isolated populations. Here, we analyze Genotype by Sequencing genomic data of the wild pumpkin C. radicans to evaluate the influence of factors like isolation, demographic history, and the environment shaping the amount and distribution of its genetic variation. We analyzed 91 individuals from 14 localities along its reported distribution. We obtained 5,107 SNPs and found medium-high levels of genetic diversity and genetic structure distributed in four main geographic areas with different environmental conditions. Moreover, we found signals of demographic growth related to historical climatic shifts. Outlier loci analysis showed significant association with the environment, principally with precipitation variables. Also, the outlier loci displayed differential changes in their frequencies in response to future global climate change scenarios. Using the results of genetic structure, outlier loci and multivariate analyses of the environmental conditions, we propose priority localities for conservation that encompass most of the genetic diversity of C. radicans.

Genome-wide identification and characterization of SNW/SKIP domain-containing proteins in plants.

Sessile organisms, such as plants, developed various ways to sense and respond to external and internal stimuli to maximize their fitness through evolutionary time. Transcripts and protein regulation are, among many, the main mechanisms that plants use to respond to environmental changes. SKIP protein is one such, presenting an SNKW interacting domain, which is highly conserved among eukaryotes, where SKI interacting protein acts in regulating key processes. In the present work, many bioinformatics tools, such as phylogenetic relationships, gene structure, physical-chemical properties, conserved motifs, prediction of regulatory cis-elements, chromosomal localization, and protein-protein interaction network, were used to better understand the genome-wide SNW/SKIP domain-containing proteins. In total, 28 proteins containing the SNW/SKIP domain were identified in different plant species, including plants of agronomic interest. Two main protein clusters were formed in phylogenetic analysis, and gene structure analysis revealed that, in general, the coding region had no introns. Also, expression of these genes is possibly induced by abiotic stress stimuli. Primary structure analysis of the proteins revealed the existence of an evolutionarily conserved functional unit. But physicochemical properties show that proteins containing the SNW/SKIP domain are commonly unstable under in vivo conditions. In addition, the protein network, demonstrated that SKIP homologues could act by modulating plant fitness through gene expression regulation at the transcriptional and post-transcriptional levels. This could be corroborated by the expression number of gene copies of SKIP proteins in many species, highlighting it's crucial role in plant development and tolerance through the course of evolution.

Use of simulation to optimize a sweet corn breeding program: implementing genomic selection and doubled haploid technology.

Genomic selection and doubled haploids hold significant potential to enhance genetic gains and shorten breeding cycles across various crops. Here, we utilized stochastic simulations to investigate the best strategies for optimize a sweet corn breeding program. We assessed the effects of incorporating varying proportions of old and new parents into the crossing block (3:1, 1:1, 1:3, and 0:1 ratio, representing different degrees of parental substitution), as well as the implementation of genomic selection in two distinct pipelines: one calibrated using the phenotypes of testcross parents (GSTC scenario) and another using F1 individuals (GSF1). Additionally, we examined scenarios with doubled haploids, both with (DH) and without (DHGS) genomic selection. Across 20 years of simulated breeding, we evaluated scenarios considering traits with varying heritabilities, the presence or absence of genotype-by-environment effects, and two program sizes (50 vs 200 crosses per generation). We also assessed parameters such as parental genetic mean, average genetic variance, hybrid mean, and implementation costs for each scenario. Results indicated that within a conventional selection program, a 1:3 parental substitution ratio (replacing 75% of parents each generation with new lines) yielded the highest performance. Furthermore, the GSTC model outperformed the GSF1 model in enhancing genetic gain. The DHGS model emerged as the most effective, reducing cycle time from 5 to 4 years and enhancing hybrid gains despite increased costs. In conclusion, our findings strongly advocate for the integration of genomic selection and doubled haploids into sweet corn breeding programs, offering accelerated genetic gains and efficiency improvements.

Genome report: First reference genome of Vaccinium floribundum Kunth, an emblematic Andean species.

Vaccinium floribundum Kunth, known as "mortiño," is an endemic shrub species of the Andean region adapted to harsh conditions in high-altitude ecosystems. It plays an important ecological role as a pioneer species in the aftermath of deforestation and human-induced fires within paramo ecosystems, emphasizing its conservation value. While previous studies have offered insights into the genetic diversity of mortiño, comprehensive genomic studies are still missing to fully understand the unique adaptations of this species and its population status, highlighting the importance of generating a reference genome for this plant. ONT and Illumina sequencing were used to establish a reference genome for this species. Three different de novo genome assemblies were generated and compared for quality, continuity and completeness. The Flye assembly was selected as the best and refined by filtering out short ONT reads, screening for contaminants and genome scaffolding. The final assembly has a genome size of 529 Mb, containing 1,317 contigs and 97% complete BUSCOs, indicating a high level of integrity of the genome. Additionally, the LTR Assembly Index of 12.93 further categorizes this assembly as a reference genome. The genome of V. floribundum reported in this study is the first reference genome generated for this species, providing a valuable tool for further studies. This high-quality genome, based on the quality and completeness parameters obtained, will not only help uncover the genetic mechanisms responsible for its unique traits and adaptations to high-altitude ecosystems but will also contribute to conservation strategies for a species endemic to the Andes.

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation.

BACKGROUND: Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family. FINDINGS: The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species. CONCLUSIONS: The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.

Genome-Wide Identification and Expression Profile Analysis of the Phenylalanine Ammonia-Lyase Gene Family in Hevea brasiliensis.

The majority of the world's natural rubber comes from the rubber tree (Hevea brasiliensis). As a key enzyme for synthesizing phenylpropanoid compounds, phenylalanine ammonia-lyase (PAL) has a critical role in plant satisfactory growth and environmental adaptation. To clarify the characteristics of rubber tree PAL family genes, a genome-wide characterization of rubber tree PALs was conducted in this study. Eight PAL genes (HbPAL1-HbPAL8), which spread over chromosomes 3, 7, 8, 10, 12, 13, 14, 16, and 18, were found to be present in the genome of H. brasiliensis. Phylogenetic analysis classified HbPALs into groups I and II, and the group I HbPALs (HbPAL1-HbPAL6) displayed similar conserved motif compositions and gene architectures. Tissue expression patterns of HbPALs quantified by quantitative real-time PCR (qPCR) proved that distinct HbPALs exhibited varying tissue expression patterns. The HbPAL promoters contained a plethora of cis-acting elements that responded to hormones and stress, and the qPCR analysis demonstrated that abiotic stressors like cold, drought, salt, and H2O2-induced oxidative stress, as well as hormones like salicylic acid, abscisic acid, ethylene, and methyl jasmonate, controlled the expression of HbPALs. The majority of HbPALs were also regulated by powdery mildew, anthracnose, and Corynespora leaf fall disease infection. In addition, HbPAL1, HbPAL4, and HbPAL7 were significantly up-regulated in the bark of tapping panel dryness rubber trees relative to that of healthy trees. Our results provide a thorough comprehension of the characteristics of HbPAL genes and set the groundwork for further investigation of the biological functions of HbPALs in rubber trees.

North American pitseed goosefoot (Chenopodium berlandieri) is a genetic resource to improve Andean quinoa (C. quinoa).

Pitseed goosefoot (Chenopodium berlandieri) is a free-living North American member of an allotetraploid complex that includes the Andean pseudocereal quinoa (C. quinoa). Like quinoa, pitseed goosefoot was domesticated, possibly independently, in eastern North America (subsp. jonesianum) and Mesoamerica (subsp. nuttaliae). To test the utility of C. berlandieri as a resource for quinoa breeding, we produced the whole-genome DNA sequence of PI 433,231, a huauzontle from Puebla, México. The 1.295 Gb genome was assembled into 18 pseudomolecules and annotated using RNAseq data from multiple tissues. Alignment with the v.2.0 genome of Chilean-origin C. quinoa cv. 'QQ74' revealed several inversions and a 4A-6B reciprocal translocation. Despite these rearrangements, some quinoa x pitseed goosefoot crosses produce highly fertile hybrids with faithful recombination, as evidenced by a high-density SNP linkage map constructed from a Bolivian quinoa 'Real-1' × BYU 937 (Texas coastal pitseed goosefoot) F2 population. Recombination in that cross was comparable to a 'Real-1' × BYU 1101 (Argentine C. hircinum) F2 population. Furthermore, SNP-based phylogenetic and population structure analyses of 90 accessions supported the hypothesis of multiple independent domestications and descent from a common 4 × ancestor, with a likely North American Center of Origin.

Genome-wide association analyses using multilocus models on bananas (Musa spp.) reveal candidate genes related to morphology, fruit quality, and yield.

Bananas (Musa spp.) are an essential fruit worldwide and rank as the fourth most significant food crop for addressing malnutrition due to their rich nutrients and starch content. The potential of their genetic diversity remains untapped due to limited molecular breeding tools. Our study examined a phenotypically diverse group of 124 accessions from the Colombian Musaceae Collection conserved in AGROSAVIA. We assessed 12 traits categorized into morphology, fruit quality, and yield, alongside sequence data. Our sequencing efforts provided valuable insights, with an average depth of about 7× per accession, resulting in 187,133 single-nucleotide polymorphisms (SNPs) against Musa acuminata (A genome) and 220,451 against Musa balbisiana (B genome). Population structure analysis grouped samples into four and five clusters based on the reference genome. By using different association models, we identified marker-trait associations (MTAs). The mixed linear model revealed four MTAs, while the Bayesian-information and linkage-disequilibrium iteratively nested keyway and fixed and random model for circulating probability unification models identified 82 and 70 MTAs, respectively. We identified 38 and 40 candidate genes in linkage proximity to significant MTAs for the A genome and B genome, respectively. Our findings provide insights into the genetic underpinnings of morphology, fruit quality, and yield. Once validated, the SNP markers and candidate genes can potentially drive advancements in genomic-guided breeding strategies to enhance banana crop improvement.

CRISPR/Cas9-Mediated Genome Editing in Indica Rice (Oryza sativa L. subsp. indica var. CR-5272).

Tissue culture optimization protocols limit indica rice breeding. Such a challenge is vital because emergent techniques still rely on tissue culture methods and could allow the breeding of new varieties with higher production and toleration of adverse environmental effects caused by climate change. Genome editing technology, using CRISPR/Cas9, is a fast and precise method for accelerated plant breeding. It limited its use in indica subspecies because of the recalcitrant response to in vitro culture methods. This chapter describes a protocol for CRISPR/Cas9 editing in indica subspecies, specifically in the CR-5272 variety derived from parental lines IR-822, using Agrobacterium tumefaciens and biolistic transformation.