scholarly journals An overview of peanut and its wild relatives

2011 ◽  
Vol 9 (01) ◽  
pp. 134-149 ◽  
Author(s):  
David J. Bertioli ◽  
Guillermo Seijo ◽  
Fabio O. Freitas ◽  
José F. M. Valls ◽  
Soraya C. M. Leal-Bertioli ◽  
...  
Keyword(s):  
Wild Species ◽  
Crop Improvement ◽  
Genomic Analysis ◽  
Linkage Drag ◽  
Root Knot Nematode ◽  
Hybrid Identities ◽  
B Genome ◽  
Cultivated Peanut ◽  
Recent Origin ◽  
The Tropics

The legumeArachis hypogaea, commonly known as peanut or groundnut, is a very important food crop throughout the tropics and sub-tropics. The genus is endemic to South America being mostly associated with the savannah-like Cerrado. All species in the genus are unusual among legumes in that they produce their fruit below the ground. This profoundly influences their biology and natural distributions. The species occur in diverse habitats including grasslands, open patches of forest and even in temporarily flooded areas. Based on a number of criteria, including morphology and sexual compatibilities, the 80 described species are arranged in nine infrageneric taxonomic sections. While most wild species are diploid, cultivated peanut is a tetraploid. It is of recent origin and has an AABB-type genome. The most probable ancestral species areArachis duranensisandArachis ipaënsis, which contributed the A and B genome components, respectively. Although cultivated peanut is tetraploid, genetically it behaves as a diploid, the A and B chromosomes only rarely pairing during meiosis. Although morphologically variable, cultivated peanut has a very narrow genetic base. For some traits, such as disease and pest resistance, this has been a fundamental limitation to crop improvement using only cultivated germplasm. Transfer of some wild resistance genes to cultivated peanut has been achieved, for instance, the gene for resistance to root-knot nematode. However, a wider use of wild species in breeding has been hampered by ploidy and sexual incompatibility barriers, by linkage drag, and historically, by a lack of the tools needed to conveniently confirm hybrid identities and track introgressed chromosomal segments. In recent years, improved knowledge of species relationships has been gained by more detailed cytogenetic studies and molecular phylogenies. This knowledge, together with new tools for genetic and genomic analysis, will help in the more efficient use of peanut's genetic resources in crop improvement.

scholarly journals ValSten: a new wild species derived allotetraploid for increasing genetic diversity of the peanut crop (Arachis hypogaea L.)

2021 ◽  
Author(s):  
Dongying Gao ◽  
Ana C. G. Araujo ◽  
Eliza F. M. B. Nascimento ◽  
M. Carolina Chavarro ◽  
Han Xia ◽  
...  
Keyword(s):  
High Resistance ◽  
Wild Species ◽  
Chromosome Doubling ◽  
Crop Improvement ◽  
Snp Array ◽  
Great Majority ◽  
Morphological Variations ◽  
Peanut Crop ◽  
Cultivated Peanut ◽  
Wild Peanut

AbstractIntrogression of desirable traits from wild relatives plays an important role in crop improvement, as wild species have important characters such as high resistance to pests and pathogens. However, use of wild peanut relatives is challenging because almost all wild species are diploid and sexually incompatible with cultivated peanut, which is tetraploid (AABB genome type; 2n = 4x = 40). To overcome the ploidy barrier, we used 2 wild species to make a tetraploid with the same allotetraploid genome composition as cultivated peanut. Crosses were made between 2 diploid wild species, Arachis valida Krapov. and W.C. Greg. (BB genome; 2n = 2x = 20) and Arachis stenosperma Krapov. and W.C. Greg. (AA genome; 2n = 2x = 20). Cuttings from the diploid F1 AB hybrid were treated with colchicine to induce chromosome doubling thus generating an induced allotetraploid. Chromosome counts confirmed polyploidy (AABB genome; 2n = 4x = 40). We named the new allotetraploid ValSten. Plants had well-developed fertile pollen, produced abundant seed and were sexually compatible with cultivated peanut. ValSten exhibits the same high resistance to early and late leaf spot and rust as its diploid parents. Notably, we observed morphological variations, including flower width and branch angles in the earliest generation (S0) of allotetraploids. A SNP array was used to genotype 47 S0 allotetraploids. The great majority of markers showed the additive allelic state from both parents (AABB). However, some loci were AAAA or BBBB, indicating homeologous recombination. ValSten provides a new, vigorous, highly fertile, disease resistant germplasm for peanut research and improvement.

scholarly journals Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

2016 ◽  
Vol 6 (12) ◽  
pp. 3825-3836 ◽  
Author(s):  
Ratan Chopra ◽  
Gloria Burow ◽  
Charles E Simpson ◽  
Jennifer Chagoya ◽  
Joann Mudge ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Wild Species ◽  
De Novo ◽  
Genome Species ◽  
Phenotypic Differences ◽  
B Genome ◽  
A Genome ◽  
Cultivated Peanut ◽  
Allele Specific ◽  
Cultivated Species

Abstract To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.

Molecular biogeographic study of recently described B- and A-genome Arachis species, also providing new insights into the origins of cultivated peanut

Genome ◽  
2009 ◽  
Vol 52 (2) ◽  
pp. 107-119 ◽  
Author(s):  
Mark D. Burow ◽  
Charles E. Simpson ◽  
Michael W. Faries ◽  
James L. Starr ◽  
Andrew H. Paterson
Keyword(s):  
Wild Species ◽  
Rflp Markers ◽  
Species Variation ◽  
Additional Species ◽  
Marker Haplotype ◽  
Genome Species ◽  
B Genome ◽  
A Genome ◽  
Cultivated Peanut ◽  
Arachis Batizocoi

The cultivated peanut Arachis hypogaea is a tetraploid, likely derived from A- and B-genome species. Reproductive isolation of the cultigen has resulted in limited genetic variability for important traits. Artificial hybridizations using selected diploid parents have introduced alleles from wild species, but improved understanding of recently classified B-genome accessions would aid future introgression work. To this end, 154 cDNA probes were used to produce 1887 RFLP bands scored on 18 recently classified or potential B-genome accessions and 16 previously identified species. One group of B-genome species consisted of Arachis batizocoi , Arachis cruziana , Arachis krapovickasii , and one potential additional species; a second consisted of Arachis ipaënsis , Arachis magna , and Arachis gregoryi . Twelve uncharacterized accessions grouped with A-genome species. Many RFLP markers diagnostic of A. batizocoi group specificity mapped to linkage group pair 2/12, suggesting selection or genetic control of chromosome pairing. The combination of Arachis duranensis and A. ipaënsis most closely reconstituted the marker haplotype of A. hypogaea, but differences allow for other progenitors or genetic rearrangements after polyploidization. From 2 to 30 alleles per locus were present, demonstrating section Arachis wild species variation of potential use for expanding the cultigen’s genetic basis.

scholarly journals Chromosome-scale genome assembly of Cucumis hystrix—a wild species interspecifically cross-compatible with cultivated cucumber

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaodong Qin ◽  
Zhonghua Zhang ◽  
Qunfeng Lou ◽  
Lei Xia ◽  
Ji Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Wild Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Comparative Genomic ◽  
Disease Resistance Gene ◽  
Introgression Breeding ◽  
Interspecific Introgression ◽  
Cucumber Genome ◽  
Cucumis Hystrix

AbstractCucumis hystrix Chakr. (2n = 2x = 24) is a wild species that can hybridize with cultivated cucumber (C. sativus L., 2n = 2x = 14), a globally important vegetable crop. However, cucumber breeding is hindered by its narrow genetic base. Therefore, introgression from C. hystrix has been anticipated to bring a breakthrough in cucumber improvement. Here, we report the chromosome-scale assembly of C. hystrix genome (289 Mb). Scaffold N50 reached 14.1 Mb. Over 90% of the sequences were anchored onto 12 chromosomes. A total of 23,864 genes were annotated using a hybrid method. Further, we conducted a comprehensive comparative genomic analysis of cucumber, C. hystrix, and melon (C. melo L., 2n = 2x = 24). Whole-genome comparisons revealed that C. hystrix is phylogenetically closer to cucumber than to melon, providing a molecular basis for the success of its hybridization with cucumber. Moreover, expanded gene families of C. hystrix were significantly enriched in “defense response,” and C. hystrix harbored 104 nucleotide-binding site–encoding disease resistance gene analogs. Furthermore, 121 genes were positively selected, and 12 (9.9%) of these were involved in responses to biotic stimuli, which might explain the high disease resistance of C. hystrix. The alignment of whole C. hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C. hystrix chromosomes. Finally, we developed four cucumber–C. hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods. The assembled C. hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.

Irrigation and crop improvement in temperate and tropical environments

1986 ◽  
Vol 316 (1537) ◽  
pp. 319-330 ◽  
Keyword(s):  
Life Cycle ◽  
Low Temperatures ◽  
Energy Use ◽  
Crop Improvement ◽  
Yield Potential ◽  
Multiple Cropping ◽  
Tropical Environments ◽  
Physiological Processes ◽  
Seasonal Signals ◽  
The Tropics

There is a strong interaction between irrigation and crop improvement, irrigation creating new opportunities and challenges for plant breeders while depending on their progress for its full benefits to be realized. In temperate environments the primary emphasis is on raising yield potential, especially as irrigation enhances the use of agrichemical inputs. Efficiency of water and energy use through the modification of physiological processes and of sensitivity to stress at various stages of the life cycle is also sought. In tropical environments, breeding for greater yield potential and more comprehensive pest and disease resistance are still important. However, shortening the length of the life cycle, reducing its sensitivity to seasonal signals and increasing yield per day may be more important than raising yield per crop because of the scope for multiple cropping made possible by irrigation in the tropics in the absence of contraints by low temperatures.

Delineating Calcium Signaling Machinery in Plants: Tapping the Potential through Functional Genomics

2021 ◽  
Vol 22 ◽  
Author(s):  
Soma Ghosh ◽  
Malathi Bheri ◽  
Girdhar K. Pandey
Keyword(s):  
Functional Genomics ◽  
Protein Kinases ◽  
Regulatory Networks ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Genomic Analysis ◽  
Major Elements ◽  
Model Systems ◽  
Plant Responses ◽  
Dependent Protein

: Plant systems have developed calcium (Ca2+) signaling as an important mechanism of regulation of stress perception, developmental cues, and responsive gene expression. The post-genomic era has witnessed the successful unravelling of the functional characterization of genes and the creation of large datasets of molecular information. The major elements of Ca2+ signaling machinery involve Ca2+ sensors and responders such as Calmodulin (CaM), Calmodulin-like proteins (CMLs), Ca2+/CaM-dependent protein kinases (CCaMK), Ca2+-dependent protein kinases (CDPKs), Calcineurin B-like proteins (CBLs) as well as transporters, such as Cyclic nucleotide-gated channels (CNGCs), Glutamate-like receptors (GLRs), Ca2+-ATPases, Ca2+/H+ exchangers (CAXs) and mechanosensitive channels. These elements play an important role in the regulation of physiological processes and plant responses to various stresses. Detailed genomic analysis can help us in the identification of potential molecular targets that can be exploited towards the development of stress-tolerant crops. The information sourced from model systems through omics approaches helps in the prediction and simulation of regulatory networks involved in responses to different stimuli at the molecular and cellular levels. The molecular delineation of Ca2+ signaling pathways could be the stepping stone for engineering climate-resilient crop plants. Here, we review the recent developments in Ca2+ signaling in the context of transport, responses, and adaptations significant for crop improvement through functional genomics approaches.

scholarly journals RECAS9: Recombining wild species introgression via mitotic gene editing in barley

2020 ◽  
Author(s):  
Shelly Lazar ◽  
Manas Ranjan Prusty ◽  
Khaled Bishara ◽  
Amir Sherman ◽  
Eyal Fridman
Keyword(s):  
Wild Species ◽  
Association Studies ◽  
Digital Pcr ◽  
Crop Wild Relatives ◽  
Linkage Drag ◽  
Genome Wide Association Studies ◽  
Starting Point ◽  
Rnp Complex ◽  
Causal Genes ◽  
The Individual

AbstractGenetic loci underlying variation in traits with agronomic importance or genetic risk factors in human diseases have been identified by linkage analysis and genome-wide association studies. However, narrowing down the mapping to the individual causal genes and variations within these is much more challenging, and so is the ability to break linkage drag between beneficial and unfavourable loci in crop breeding. We developed RECAS9 as a transgene-free approach for precisely targeting recombination events by delivering CRISPR/Cas9 ribonucleotide protein (RNP) complex into heterozygous mitotic cells for the barley (Hordeum vulgare) Heat3.1 locus. A wild species (H. spontaneum) introgression in this region carries the agronomical unfavourable tough rachis phenotype (non-brittle) allele linked with a circadian clock accelerating QTL near GIGANTEA gene. We delivered RNP, which was targeted between two single nucleotide polymorphism (SNPs), to mitotic calli cells by particle bombardment. We estimated recombination events by next generation sequencing (NGS) and droplet digital PCR (ddPCR). While NGS analysis grieved from confounding effects of PCR recombination, ddPCR analysis allowed us to associate RNP treatment on heterozygous individuals with significant increase of homologous directed repair (HDR) between cultivated and wild alleles, with recombination rate ranging between zero to 57%. These results show for the first time in plants a directed and transgene free mitotic recombination driven by Cas9 RNP, and provide a starting point for precise breeding and fine scale mapping of beneficial alleles from crop wild relatives.

Flavor Profiles of Wild Species-Derived Peanut Breeding Lines

2008 ◽  
Vol 35 (2) ◽  
pp. 81-85 ◽  
Author(s):  
S. P. Tallury ◽  
H. E. Pattee ◽  
T. G. Isleib ◽  
H. T. Stalker
Keyword(s):  
Wild Species ◽  
Interspecific Hybrid ◽  
Diploid Species ◽  
Sensory Attributes ◽  
Sources Of Resistance ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Arachis Hypogaea L ◽  
Cultivated Peanut ◽  
Important Quality

Abstract Several diploid wild species of the genus Arachis L. have been used as sources of resistance to common diseases of cultivated peanut (Arachis hypogaea L.). Because flavor is among the most important quality attributes for commercial acceptance of roasted peanuts, sensory attributes of interspecific hybrid derived breeding lines were evaluated to determine if transfer of disease resistance from wild species is associated with concomitant changes in flavor. Sixteen interspecific hybrid derivatives with five diploid species in their ancestries and the commercial flavor standard, NC 7 were evaluated for sensory quality. Significant variation among entries was found for the roasted peanut, sweet, and bitter sensory attributes, but not for the overall contrast between NC 7 and the wild species-derived breeding lines. The variation was either between two groups of wild species-derived breeding lines or within one or both groups. Introduction of disease and pest resistance traits from Arachis species did not result in degradation or improvement of the flavor profile. This suggests that flavor of wild species-derived germplasm will not prevent its use either as parents in peanut breeding programs or as cultivars.

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