Crop Evolution Research Articles

Lentil Breeding: Present State and Future Prospects

Lentil (Lens culinaris Medik.) is one of the vital grain legume crops that originated from L. culinaris Medik.ssp. orientalisin the Near East. It is an essential food source that is capable of contributing energy, proteins and iron to human diet. Major concern of lentil producing countries is to have a stable high seed yield in addition to resistance against abiotic and biotic stresses. The activities of domestication and selection in the course of crop evolution have led to reduction in genetic variation in the current cultivars and species, which is a major drawback for lentil breeding. The improvement of many monogenic traits has been carried out by conventional breeding techniques like selection and recombination. However, these improvements still lack in addressing economic traits like yield as they are governed by polygenes and G x E interaction. Various species in the genus Lens can aid to enhancement of genetic variation for target lentil traits to develop new varieties. Induced mutagenesis is another vital breeding method which can ease the availability of lentil genomic resources. Commendable success stories in applications of molecular markers and biotechnological techniques will further speed-up the development of improved varieties. This review article majourly dealt on present status on genetic improvement in lentil and a compendium of important aspects of lentil diversity, genetics and breeding with the way forward.

Recombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet

We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones.

Cucurbitaceae genome evolution, gene function and molecular breeding.

Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation, and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae, and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationships, and functional genes associated with important agronomic traits (e.g. fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.

Automatic Large-Scale Precise Mapping and Monitoring of Agricultural Fields at Country Level With Sentinel-2 SITS

Availability of multitemporal (MT) images, such as the sentinel-2 (S2) ones, offers accurate spatial, spectral and temporal information to effectively monitor vegetation, more specifically agriculture. Agricultural practices can benefit from temporally dense satellite image time series (SITS) for accurate understanding of the phenological evolution and behavior of crops. Developing techniques that deal with high spatial correlation and high temporal resolution requires a shift in the processing paradigm and poses new challenges in terms of data processing and methodology. This article presents an automatic approach to large-scale precise mapping of small agricultural fields based on the analysis of S2-SITS at Country level. The approach deals with a flexible and automatic processing chain for massive data and was tested at Country level. The large-scale application requires to consider: the management of big amount of data with particular attention to download and pre-processing of S2-SITS; and MT fine characterization of crop fields accounting for the strong variability in size and phenological behaviors when mapping at large scale. Both challenges are addressed in an automatic way by exploiting and/or updating state-of-the-art methodologies. Promising results have been obtained and validated over 2017 and 2018 agrarian years for Italy.

Genome Editing and Designer Crops for the Future.

Domestication spanning over thousands of years led to the evolution of crops that are being cultivated in recent times. Later, selective breeding methods were practiced by human to produce improved cultivars/germplasm. Classical breeding was further transformed into molecular- and genomics-assisted breeding strategies, however, these approaches are labor-intensive and time-consuming. The advent of omics technologies has facilitated the identification of genes and genetic determinants that regulate particular traits allowing the direct manipulation of target genes and genomic regions to achieve desirable phenotype. Recently, genome editing technologies such as meganucleases (MN), zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-Associated protein 9 (Cas9) have gained popularity for precise editing of genes to develop crop varieties with superior agronomic, physiological, climate-resilient, and nutritional traits. Owing to the efficiency and precision, genome editing approaches have been widely used to design the crops that can survive the challenges posed by changing climate, and also cater the food and nutritional requirements for ever-growing population. Here, we briefly review different genome editing technologies deployed for crop improvement, and the fundamental differences between GE technology and transgene-based approach. We also summarize the recent advances in genome editing and how this radical expansion can complement the previously established technologies along with breeding for creating designer crops.

Population genomic analysis reveals domestication of cultivated rye from weedy rye

Rye (Secale cereale) is an important crop with multiple uses and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. The geneticist N.I. Vavilov proposed that cultivated rye had been domesticated from weedy rye, rather than directly from wild species like other crops. Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds. To this end, in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild, weedy, and cultivated rye, and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans. We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits, including shattering, grain yield, and disease resistance. Furthermore, we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye. Taken together, our findings unravel the domestication history of cultivated rye, suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale, and provide an important resource for future rye and wheat breeding.

Oil plant genomes: current state of the science.

Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.

Role of Molecular Markers in Crop Breeding: A Review

Molecular markers are effective tools used to ‘flag’ the location of a specific gene or the inheritance of a definite trait. Markers are unique DNA fragments that can be identified inside the entire genome. The development of molecular markers combined with high throughput technologies have paved the way for achieving the desirable traits as well as induced biotic and abiotic stress tolerance in plant, which enhanced the crop breeding. Highly polymorphic molecular markers are developed for gene mapping, estimation of genetic diversity, finding out the evolution and phylogeny of crop, analysis of heterosis, assessment of diploid/haploid crops and genotyping of cultivars along with Marker Assisted Breeding (MAB)/Marker Assisted Selection (MAS). These are the most significant objectives for crop breeding. This review reveals about the role of various recently developed molecular markers in the improvement of crop. Molecular markers act as a “milestone” for the researchers who aim to enhance crop breeding.

Polyploidization and domestication

<p indent=0mm>Crop domestication is the process to domesticate and propagate wild plants into cultivated crops, and its essence is to purposefully preserve the genetic variation information on the genome through artificial selection. Domestication has played an important role in the origin and evolution of human farming civilization, and promoted the sustainable development of human civilization and the rapid progress of society, in which polyploidization is an important direction of crop domestication and improvement. Compared with the diploid ancestor species, polyploid crops often have obvious phenotypic advantages, relatively high biomass and economic yield, stronger resistance, as well as wider environmental adaptability. Important crops such as wheat (<italic>Triticum aestivum</italic> L.), cotton (<italic>Gossypium </italic>spp.), rape (<italic>Brassica napus</italic> L.) and potato (<italic>Solanum tuberosum </italic>L.) have experienced a long evolutionary process, and are comprehensive products of polyploidization and domestication. The evolution and domestication of polyploid crops and the molecular mechanism of important agronomic traits have always been important scientific issues in the field of crop genetics and breeding, which is of great significance for the molecular design and breeding of crops and sustainable development of agriculture.

Effects of Different Types of Fertilizers on Rice Productivity in the Irrigated Perimeter of Toula (Niger)

AIM: Assessment of various fertilizers type effects on rice productivity in Niger.&#x0D; Study Design: The experiment was laid by using a complete randomized block design with different types of fertilizers and was replicated four times.&#x0D; Place and Duration of Study: The field experiment was conducted during the dry and wet season of 2020 on the irrigated perimeter of Toula (Niger).&#x0D; Methodology: The experiment was performed with four treatments in complete randomized blocks. The treatments applied are: T1=Bokashi, T2=Compost, T3=Biochar and T4=NPK-Urea. The monitored parameters were the rice plant development cycle and agronomic characteristics. Observations of the crop evolution during the experimentation were recorded at regular intervals. The significance of treatment impact was examined by the statistical test. &#x0D; Results: The results showed that bio-fertilizers had significant effects on 1000 grain weight and the length of the vegetative cycle. As for the chemical treatments, the effects were significant on most of the rice growth parameters (height, number of grains per panicle, number of tillers per rice plant) as well as on paddy and feed biomass yield. These results also showed a positive correlation between rice growth parameters and yield irrespective of the type of treatment.

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.

The genomes of ancient date palms germinated from 2,000 y old seeds

Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to modern West Asian date varieties, but later material from the second century BCE to second century CE showed increasing genetic affinities to present-day North African date palms. Population genomic analysis reveals that by ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in the Eastern Mediterranean already contained introgressed segments from the Cretan palm Phoenix theophrasti, a crucial genetic feature of the modern North African date palm populations. The P. theophrasti introgression fraction content is generally higher in the later samples, while introgression tracts are longer in these ancient germinated date palms compared to modern North African varieties. These results provide insights into crop evolution arising from an analysis of plants originating from ancient germinated seeds and demonstrate what can be accomplished with the application of a resurrection genomics approach.

Effects of crop evolution under domestication and narrowing genetic bases of crop species

Crop improvement is very crucial to satisfy the world demand in the presence of different challenges like climate change, reducing arable land and increasing population growth.

De-Domestication: An Extension of Crop Evolution.

De-domestication or feralization is an interesting phenomenon in crops and livestock. Previously, evidence for crop de-domestication was based mainly on studies using phenotypic and genotypic data from limited molecular markers or gene segments. Recent genomic studies in rice, barley, and wheat provide comprehensive landscapes of de-domestication on a whole-genome scale. Here, we summarize crop de-domestication processes, ecological roles of de-domesticates, mechanisms underlying crop de-domestication syndromes, and conditions potentially favoring de-domestication events. We further explain how recent de-domestication studies have expanded our understanding of the complexity of crop evolution, and highlight the genetic novelties of de-domesticates beneficial for modern crop breeding.

Ancient relaxation of an obligate short-day requirement in common bean through loss of CONSTANS-like gene function

Common bean (Phaseolus vulgaris L.) is a major global food staple and source of dietary protein that was domesticated independently in Mexico and Andean South America. Its subsequent development as a crop of importance worldwide has been enabled by genetic relaxation of the strict short-day requirement typical of wild forms, but the genetic basis for this change is not well understood. Recently, a loss of photoperiod sensitivity was shown to result from mutations in the phytochrome photoreceptor gene Ppd/PHYA3 that arose independently within the two major domesticated lineages. Here, we define a second major photoperiod sensitivity locus, at which recessive alleles associate with deleterious mutations affecting the CONSTANS-like gene COL2. A wider survey of sequence variation in over 800 diverse lines, including wild, landrace, and domesticated accessions, show that distinct col2 haplotypes are associated with early flowering in Andean and Mesoamerican germplasm. The relative frequencies and distributions of COL2 and PHYA3 haplotypes imply that photoperiod adaptation developed in two phases within each gene pool: an initial reduction in sensitivity through impairment of COL2 function and subsequent complete loss through PHYA3. Gene expression analyses indicate that COL2 functions downstream of PHYA3 to repress expression of FT genes and may function in parallel with PvE1, the bean ortholog of a key legume-specific flowering repressor. Collectively, these results define the molecular basis for a key phenological adaptation, reveal a striking convergence in the naturally replicated evolution of this major crop, and further emphasize the wider evolutionary lability of CONSTANS effects on flowering time control.

Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment.

Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.

Natural Variation in Crops: Realized Understanding, Continuing Promise.

Crops feed the world's population and shape human civilization. The improvement of crop productivity has been ongoing for almost 10,000 years and has evolved from an experience-based to a knowledge-driven practice over the past three decades. Natural alleles and their reshuffling are long-standing genetic changes that affect how crops respond to various environmental conditions and agricultural practices. Decoding the genetic basis of natural variation is central to understanding crop evolution and, in turn, improving crop breeding. Here, we review current advances in the approaches used to map the causal alleles of natural variation, provide refined insights into the genetics and evolution of natural variation, and outline how this knowledge promises to drive the development of sustainable agriculture under the dome of emerging technologies.

Next generation breeding in pulses: Present status and future directions

Human population growth in combination with changing patterns of global food consumption under climate change is posing formidable challenge to attaining sustainable global food security. Besides being economically viable sources of plant based protein for human consumption, pulses are also beneficial for the environment owing to their inherent capacity of nitrogen fixation. Hence, further development of pulses has become imperative in the vigorously transitional global scenario where flourishing anthropogenic activities are triggering irreplaceable depletion of natural resources. During past years, considerable attention has been given on the use of next generation sequencing for enriching the genomic resources in pulse crops including high-throughput DNA markers, candidate gene(s) and QTLs for predicting plant phenotypes, and whole genome sequences. With refinements in DNA sequencing technologies and computational analytical tools, the rapidly grown numbers of sequenced pulse genomes offer novel insights on crop evolution and breeding history. Integration of new-generation genomic and phenomic tools with generation acceleration procedures like genomic selection and speed breeding could greatly accelerate progress in pulses genetic improvement. The present review discusses current status and future scope of using next-generation breeding approaches in pulses that will cause not only an increase in the rate of developing climate-resilient superior cultivars but also help to reach to goal of global food security.

The lowest hanging fruit: Beneficial gene knockouts in past, present, and future crop evolution

It is now well-documented that gene knockout (loss-of-function) alleles have played a prominent role in crop evolution during domestication, diversification, and improvement. This includes dramatic examples from the very origins of agriculture to the monumental yield increases of the Green Revolution. Recent advances in the generation of whole genome sequence data and functional investigations into the molecular genetic basis of crop traits continue to reveal the existence of considerable beneficial loss of function in crop species. These discoveries now inspire contemporary efforts to use targeted gene knockouts powered by modern gene editing tools to accelerate crop breeding. Here we trace the history and future of loss of function as a powerful mechanism of crop evolution and review the reasons gene knockouts might have been particularly important in past crop evolution and why they continue to be a “lowest hanging fruit” for directing crop evolution through molecular breeding in pursuit of more productive, resilient, and nutritious crops.

Quantitative trait loci for horticulturally important traits defining the Sikkim cucumber, Cucumis sativus var. sikkimensis.

QTL mapping identified simply inherited genes and quantitative trait loci underlying morphologically characteristic traits of the Sikkim cucumber, which reveals their genetic basis during crop evolution. The data suggest the Sikkim cucumber as an ecotype of cultivated cucumber not worthy of formal taxonomic recognition. The Sikkim cucumber, Cucumis sativus var. sikkimensis, is featured with some morphological traits like black spine, brown fruit with fine and heavy netting, as well as large hollow in mature fruit. Despite its establishment as a botanical variety ~ 150years ago, and its wide use as an important source of disease resistances in cucumber breeding, little is known about its taxonomic status and genetic basis of those characteristic traits. Here we reported QTL mapping with segregating populations derived from two Sikkim-type inbred lines, WI7088D and WI7120, and identification of 48 QTL underlying phenotypic variation for 18 horticulturally important traits. We found that the fruit spine and skin colors in the two populations were controlled by the previously cloned pleiotropic B (black spine) locus. The fruit netting in WI7088D and WI7120 was controlled by the well-known H (Heavy netting) and a novel Rs (Russet skin) locus, which was delimited to a 271-kb region on Chr5 and ~ 736-kb region on Chr1, respectively. A single major-effect QTL was detected for flowering time in each population (ft1.1 for WI7088D and ft6.2 for WI7120). Fifteen, six and five QTL were identified for fruit size, hollow size and flesh thickness variation in the two populations, respectively. No major structural changes were found between the Sikkim and cultivated cucumbers. Except for the rare allele at the Rs locus, there seem no private QTL/alleles identified from this study supporting the Sikkim cucumber as an ecotype of C. sativus, not worthy of formal taxonomic recognition.