A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include , , and , which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the "domestication alleles" of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the and alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the and domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the , , and alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered.

A recently developed synthetic amphiploid, Kost., nom. nud. (2n = 6x = 42, AAGGAA) is described in the present study. This hexaploid taxon was developed by colchicine treatment in Martonvásár from the hybrid of a selected accession of Zhuk. (2n = 4x = 28, AAGG) and a prebred semi-dwarf line of L. (2n = 2x = 14, AA). A detailed cytomolecular examination was carried out using the sequential multicolour fluorescence and genomic hybridization techniques (FISH and mcGISH). It was proved that has 42 chromosomes originating from its parents. The chromosomes of the A genomes of and could be distinguished in the amphiploid using FISH. The successful discrimination of the chromosomes was supported by the karyotypes of the three genomes and the successful optimization of the mcGISH technique for the A and G chromosomes achieved in the present study. A phenotypic evaluation was also carried out under natural and artificial growing conditions in 2012 and 2013. Based on the results, has intermediate characteristics in terms of spike (spikelet) shape and plant height, while it is similar to the female parent, regarding pubescence. Like its parents, showed outstanding resistance to the main fungal diseases of wheat. headed later and developed longer and looser spikes, fewer tillers and only a third as many seeds than its parents. The third generation of was able to develop an acceptable number of seeds, even taking into account the reduced germination ability in the field.

Common bean ( L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools.

Morphological traits are commonly used for characterizing plant genetic resources. Germplasm characterization should be based on distinctly identifiable, stable and heritable traits that are expressed consistently and are easy to distinguish by the human eye. Characterization and documentation of a representative sample of East African highland bananas (Lujugira-Mutika subgroup) was carried out following an internationally accepted standard protocol for bananas. Eleven cultivars were characterized using an existing set of minimum descriptors (31 qualitative and quantitative traits) with the aim of determining stable descriptors and the ability of these descriptors to distinguish among East African highland banana cultivars. There was variation in stability of these descriptors within cultivars and across the 11 cultivars. Only 10 (32%) out of 31 descriptors studied were stable in the 11 cultivars. However, they had similar scores and therefore are not suitable to distinguish between cultivars within this group. Nonetheless, these 10 descriptors may be useful for distinguishing the East African highland bananas as a group from other groups of bananas. A few descriptors were unique to the cultivar 'Tereza' and may be used to distinguish this cultivar from other 'matooke' cultivars. None of the quantitative descriptors were stable.

Crevost & Lemarié is an important crop that has been widely used in traditional Chinese medicine and daily diets for a long time. In this study, the genetic diversity and relationships of eight cultivated populations of grown in Southwest China were examined using sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. The results showed that 139 (99.29%) of 140 and 185 (99.46%) of 186 bands were polymorphic by SRAP and ISSR primers amplification, respectively. The polymorphic information content of detected bands were 0.270 (SRAP) and 0.232 (ISSR), respectively. The average Nei's gene diversity (H = 0.217) and Shannon's information index (I = 0.348) at the species level generated by SRAP primer were higher than those by ISSR analysis (H = 0.158, I = 0.272). Genetic differentiation coefficients and molecular variance analysis (AMOVA) indicated that the genetic variance of mainly occurred within populations rather than among populations. The high genetic identity among populations was revealed by SRAP (0.937) and ISSR (0.963). Using UPGMA cluster analysis, principal coordinate analysis, and population structure analysis, the accessions were categorized into two major groups. Overall, results obtained here will be useful for germplasm characterization, conservation, and utilization.

Groundnut ( L.) is a multi-purpose legume serving millions of farmers and their value chain actors globally. Use of old poor-performing cultivars contributes to low yields (< 1 t/ha) of groundnut in sub-Saharan Africa including Tanzania. The objectives of this study were to determine the extent of genetic variation among diverse groundnut collections using phenotypic traits and simple sequence repeat (SSR) markers to select distinct and complementary genotypes for breeding. One hundred and nineteen genotypes were evaluated under field conditions for agronomic traits and susceptibility to rust and leaf spot diseases. The study was conducted in two locations across two seasons. In addition, the 119 accessions were profiled with 13 selected SSR markers. Genotype and genotype by environment interaction effects were significant ( < 0.05) for days to flowering (DTF), late leaf spot score at 85 and 100 days after planting, pod yield (PDY), kernel yield (KY), hundred seed weight (HSW) and shelling percentage (SP). Principal components analysis revealed that plant stand, KY, SP, NPP (number of pods per plant), late leaf spot and rust disease scores accounted for the largest proportion of the total variation (71.9%) among the tested genotypes. Genotypes ICGV-SM 08587 and ICGV-SM 16579 had the most stable yields across the test environments. Moderate genetic variation was recorded with mean polymorphic information content of 0.34 and gene diversity of 0.63 using the SSR markers. The majority (74%) of genotypes showed high membership coefficients to their respective sub-populations, while 26% were admixtures after structure analysis. Much of the variation (69%) was found within populations due to genotypic differences. The present study identified genotypes ICGV-SM 06737, ICGV-SM 16575, ICG 12725 and ICGV-SM 16608 to be used for development of mapping population, which will be useful for groundnut improvement. This study provided a baseline information on characterization and selection of a large sample of groundnut genotypes in Tanzania for effective breeding and systematic conservation.

Lablab () [ (L.) Sweet] is termed a lost, underutilized and neglected crop in Africa. Despite the multipurpose use, production, consumption and research are still limited. Wide genetic diversity of lablab germplasm exists in Africa. Diversity studies provide significant information for subsequent research programs and improvement. The advent of genotyping and sequencing technologies has enabled the identification of unique and agronomically important traits. Application of next-generation sequencing on lablab as a pioneer orphan crop is currently underway. This has enabled description of the whole genome, generation of reference genome and resequencing that provide information on variation within the entire genome. Information from these technological advances helps in identifying potential traits for biotic and abiotic stress for further breeding programs. Storage pests specifically bruchids ( spp.), are considered a major obstacle in lablab production. Screening of available genotypes for bruchid resistance and studies on the physical and biochemical factors that confer resistance in lablab is required. Applying advanced technologies provides precise and reliable identification of the novel markers responsible for bruchid resistance allowing for introgression of important genes to breeding programs. This review provides a detailed analysis on the characterization of lablab and the information on bruchid resistance vital for breeding farmer-preferred varieties that possess agronomically beneficial traits. Concerted efforts and research on this neglected crop will enhance its production, utilization and consumption.

A wide array of medicinal plants in India, primarily used by locals for health care, have found wide acceptance and adoption globally (either directly or processed) due to distinct advantages of good results, low or no side-effects and ease of access to general public. Indigenous and traditional systems of medicine in practice since historical times have shown potential (direct or indirect as immune-boosters) against many dreaded ailments including the recent global pandemic of COVID-19. With prediction of sixth mass extinction, there is worldwide concern as majority of these plants, collected from natural stands, are also facing threat of extinction. Since 1990s concerted efforts have been directed towards assessment of threat status, the basic requirement for prioritizing conservation activity to various species of plants and animals. In literature there is staggered information regarding list of threatened plants, including medicinal plants of India, compiled at either state level or national or international level. Analysis of these publications led to collation of a consolidated list of 84 species and the same is presented here. A brief account of conservation efforts in India at national level and supportive policy framework is also included. This compilation is aimed to serve as a comprehensive reference especially for beginners, researchers, conservationists, foresters, pharmaceutical professionals as well as policy makers.

 Gomes is a fruit and medicinal tree species native to South America, which in Brazil is considered of potential economic value and priority for research and development. We present a map of the state-of-art, including articles, patents, and molecular data of the species to identify perspectives for future research. The annual scientific production, intellectual, social, and conceptual structure were evaluated, along with the number of patent deposits, components of the plant used, countries of deposit, international classification and assignees, and the accessibility of available molecular data. Brazil has the most significant publications (306) between 1992 and 2020. Technological products (29) have been developed from different tissues of the plant. Most of the articles and patents were developed by researchers from public universities from different regions of Brazil. The molecular data are sequences of nucleotides (164) and proteins (236) of the chloroplast genome and are described to identify the species as DNA barcodes and proteins involved in photosynthesis. The compilation and report of scientific, technological, and molecular information in the present review allowed the identification of new perspectives of research to be developed based on the gaps in knowledge regarding the species and perspectives for the definition of future research.

Most orphan crops have not been fully sequenced, hence we rely on genome sequences of related species to align markers to different chromosomes. This hinders their utilisation in plant population improvement programs. Utilising the advances in the science of sequencing technologies, the population structure, relatedness, and genetic diversity among accessions can be assessed quickly for better exploitation in forage breeding programs. Using DArTseq technology, we studied the genetic and structural variation in 65 (L.) Sweet conserved gene-bank accessions using 9320 DArTseq-based SNPs and 15,719 SilicoDart markers. These markers had a low discriminating ability with mean polymorphic information content (P.I.C.) of 0.14 with DArTseq-based SNPs and 0.13 with SilicoDart markers. However, the markers had a high mean call rate of 73% with DArTseq-based SNPs and 97% with SilicoDart markers. Analysis of molecular variance revealed a high within populations variance (99.4%), indicating a high gene exchange or low genetic differentiation (PhiPT = 0.0057) among the populations. Structure analysis showed three allelic pools in variable clusters of ΔK = 3 and 6. Phylogenetic tree of lablab accessions showed three main groups with variable membership coefficients. Most pairs of accessions (40.3%) had genetic distances between 0.10 and 0.15 for SilicoDart markers, while for DArTseq-based SNPs, (46.5%) had genetic distances between 0.20 and 0.25. Phylogenetic clustering and minimum spanning analysis divided the 65 accessions into three groups, irrespective of their origin. For the first time, this study produced high-density markers with good genom coverage. The utilisation of these accessions in a forage program will base on the information from molecular-based grouping. The outcomes uncovered the presence of noteworthy measure of variety in Uganda, CIAT and ILRI accessions, thus demonstrating an opportunity for further marker-trait-association studies.

Garlic is a vegetable widely used both in food and as a pharmaceutical raw material in the world due to its contents. Although morphological differences are observed in garlic, which is obligatory apomictically propagated, clonal propagation causes narrowing variation, a genetic bottleneck. This situation complicates breeding programs aiming improvements in preferred agronomic characteristics. For this reason, determining the morphological and molecular differences between garlic genotypes originating from Turkey is important for breeding studies. In this study, morphological and molecular characteristics of 39 garlic genotypes, which are widely cultivated in Turkey, were determined. Kahramanmaraş4 genotype was different from other genotypes in terms of some morphological features (fresh weight, dry weight, and bulb diameter). In the molecular characterization study, 10 Inter-Simple Sequence Repeats (ISSR) primers were used, and it was determined that the genotype TekDiş31 of Tunceli region was different from other garlic genotypes. Genetic similarity coefficient was found to be high (0.85-1.0) in genotypes except for TekDiş31 garlic genotype. In general, some garlic clones (Maraş3 and Kayseri30, Urfa33 and Topaklı35, Kastamonu22 and Kastamonu28, Urfa10 and Kastamonu14, Kastamonu29 and Bademci23) were completely similar to each other, while few differences were found among others. In conclusion, this study revealed that the garlic plant, despite its clonal propagation, consisted of some level of morphological and partially molecular variation. Due to its mode of reproduction (vegetative), this variation may largely be due to point or chromosomal mutation. Furthermore, the 10 identified ISSR primers can generate valuable information for genetic diversity for use by garlic breeders.

Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of across its distribution range using microsatellite markers. Accessions stored at the International Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild . Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes.

Sugarcane ( spp.) is a special crop plant that underwent anthropogenic evolution from a wild grass species to an important food, fodder, and energy crop. Unlike any other grass species which were selected for their kernels, sugarcane was selected for its high stem sucrose accumulation. Flowering in sugarcane is not favored since flowering diverts the stored sugar resources for the reproductive and developmental energy needs. Cultivars are vegetatively propagated and sugarcane breeding is still essentially focused on conventional methods, since the knowledge of sugarcane genetics has lagged that of other major crops. Cultivar improvement has been extremely challenging due to its polyploidy and aneuploidy nature derived from a few interspecific hybridizations between and revealing the coexistence of two distinct genome organization modes in the modern variety. Alongside implementation of modern agricultural techniques, generation of hybrid clones, transgenics and genome edited events will help to meet the ever-growing bioenergy needs. Additionally, there are two common biotechnological approaches to improve plant stress tolerance, which includes marker-assisted selection (MAS) and genetic transformation. During the past two decades, the use of molecular approaches has contributed greatly to a better understanding of the genetic and biochemical basis of plant stress-tolerance and in some cases, it led to the development of plants with enhanced tolerance to abiotic stress. Hence, this review mainly intends on the events that shaped the sugarcane as what it is now and what challenges ahead and measures taken to further improve its yield, production and maximize utilization to beat the growing demands.

Fresh pods are harvestable and marketable economic product in dolichos bean. Fresh pod fragrance is one of the 'farmers' and 'consumers' preferred traits in dolichos bean varieties. The pods with high fragrance fetch a premium price in the market. In breeding programmes, pod fragrance is routinely assessed by organoleptic (sensory) means, which is highly relative and subjective. Identification of linked DNA markers not only offer an objective means but also enable selection of fragment genotypes at seedling stage itself. Betaine aldehyde dehydrogenase () is known to be the key gene responsible for fragrance in other legumes such as vegetable soybean and mung bean. Taking cues from highly conserved domains in proteins coded by genes, we isolated dolichos bean homolog () of soybean gene using reported degenerate primers designed to conserved domains. Analysis of the translated amino acid sequence of showed high degree of similarity (97.30%) with those of soybean homolog (). Conserved amino acid sequence of aldehyde dehydrogenase-super family were also identified in . Multiple sequence alignment of nucleotide sequences of with those of related legumes using "ClustalW" revealed the presence of a single non-synonymous single nucleotide polymorphic (SNPs) and three synonymous SNP sites in The substitution of the amino acid tyrosine in (fragrant genotypes) with phenyl alanine (non-fragrant genotypes) in protein coded by appeared to be the cause for switch over from fragrance to non-fragrance in dolichos bean. These results are discussed in relation to strategies to breed dolichos bean cultivars with desired level of pod fragrance.

Breeding for host resistance is the most efficient and environmentally safe method to curb the spread of fusarium ear rot (FER). However, conventional breeding for resistance to FER is hampered by the complex polygenic nature of this trait, which is highly influenced by environmental conditions. This study aimed to identify genomic regions, single nucleotide polymorphisms (SNPs), and putative candidate genes associated with FER resistance as well as candidate metabolic pathways and pathway genes involved in it. A panel of 151 tropical inbred maize lines were used to assess the genetic architecture of FER resistance over two seasons. During the study period, seven SNPs associated with FER resistance were identified on chromosomes 1, 2, 4, 5, and 9, accounting for 4-11% of the phenotypic variance. These significant markers were annotated into four genes. Seven significant metabolic pathways involved in FER resistance were identified using the Pathway Association Study Tool, the most significant being the superpathway of the glyoxylate cycle. Overall, this study confirmed that resistance to FER is indeed a complex mechanism controlled by several small to medium-effect loci. Our findings may contribute to fast-tracking the efforts to develop disease-resistant maize lines through marker-assisted selection.