scholarly journals Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

Plant Methods ◽  
2022 ◽  
Vol 18 (1) ◽  
Author(s):  
Zhenquan Duan ◽  
Yongli Zhang ◽  
Tian Zhang ◽  
Mingwei Chen ◽  
Hui Song
Keyword(s):  
Arachis Hypogaea ◽  
Ion Homeostasis ◽  
Purifying Selection ◽  
Evolutionary Patterns ◽  
Proteomic Data ◽  
Tandem Mass Tag ◽  
Cultivated Peanut ◽  
Aa Genome ◽  
Root Tissues ◽  
Differentially Abundant Proteins

Abstract Background Cultivated peanut (Arachis hypogaea, AABB genome), an allotetraploid from a cross between A. duranensis (AA genome) and A. ipaensis (BB genome), is an important oil and protein crop with released genome and RNA-seq sequence datasets. These datasets provide the molecular foundation for studying gene expression and evolutionary patterns. However, there are no reports on the proteomic data of A. hypogaea cv. Tifrunner, which limits understanding of its gene function and protein level evolution. Results This study sequenced the A. hypogaea cv. Tifrunner leaf and root proteome using the tandem mass tag technology. A total of 4803 abundant proteins were identified. The 364 differentially abundant proteins were estimated by comparing protein abundances between leaf and root proteomes. The differentially abundant proteins enriched the photosystem process. The number of biased abundant homeologs between the two sub-genomes A (87 homeologs in leaf and root) and B (69 and 68 homeologs in leaf and root, respectively) was not significantly different. However, homeologous proteins with biased abundances in different sub-genomes enriched different biological processes. In the leaf, homeologs biased to sub-genome A enriched biosynthetic and metabolic process, while homeologs biased to sub-genome B enriched iron ion homeostasis process. In the root, homeologs with biased abundance in sub-genome A enriched inorganic biosynthesis and metabolism process, while homeologs with biased abundance in sub-genome B enriched organic biosynthesis and metabolism process. Purifying selection mainly acted on paralogs and homeologs. The selective pressure values were negatively correlated with paralogous protein abundance. About 77.42% (24/31) homeologous and 80% (48/60) paralogous protein pairs had asymmetric abundance, and several protein pairs had conserved abundances in the leaf and root tissues. Conclusions This study sequenced the proteome of A. hypogaea cv. Tifrunner using the leaf and root tissues. Differentially abundant proteins were identified, and revealed functions. Paralog abundance divergence and homeolog bias abundance was elucidated. These results indicate that divergent abundance caused retention of homologs in A. hypogaea cv. Tifrunner.

scholarly journals Diversity in Nutrient Content and Consumer Preferences of Sensory Attributes of Peanut (Arachis hypogaea L.) Varieties in Ugandan Agroecosystems

2021 ◽  
Vol 13 (5) ◽  
pp. 2658
Author(s):  
Rose Nankya ◽  
John W. Mulumba ◽  
Hannington Lwandasa ◽  
Moses Matovu ◽  
Brian Isabirye ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Consumer Preferences ◽  
Consumer Preference ◽  
Nutrient Content ◽  
Intraspecific Diversity ◽  
Laboratory Evaluation ◽  
Organoleptic Characteristics ◽  
Arachis Hypogaea L ◽  
Cultivated Peanut ◽  
Nutrient Amounts

The cultivated peanut (Arachis hypogaea L.) is one of the most widely consumed legumes globally due to its nutrient content, taste, and affordability. Nutrient composition and consumer preference were determined for twenty local farmer (landrace) and commercial peanut varieties grown in the Nakaseke and Nakasongola districts of the central wooded savanna of Uganda through sensory and laboratory evaluation. Significant differences in nutrient content (p < 0.05) among peanut varieties were found within and across sites. A significant relationship between nutrient content and consumer preference for varieties within and across sites was also realized (Wilk’s lambda = 0.05, p = 0.00). The differences in nutrient content influenced key organoleptic characteristics, including taste, crunchiness, appearance, and soup aroma, which contributed to why consumers may prefer certain varieties to others. Gender differences in variety selection were significantly related to consumer preference for the crunchiness of roasted peanut varieties (F = 5.7, p = 0.016). The results imply that selecting different varieties of peanuts enables consumers to receive different nutrient amounts, while experiencing variety uniqueness. The promotion of peanut intraspecific diversity is crucial for improved nutrition, organoleptic appreciation and the livelihood of those engaged in peanut value chains, especially for the actors who specialize in different peanut products. The conservation of peanut diversity will ensure that the present and future generations benefit from the nutritional content and organoleptic enjoyment that is linked to unique peanut varieties.

scholarly journals Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals

2016 ◽  
Vol 113 (21) ◽  
pp. E2983-E2992 ◽  
Author(s):  
Pierre Boudinot ◽  
Stanislas Mondot ◽  
Luc Jouneau ◽  
Luc Teyton ◽  
Marie-Paule Lefranc ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Purifying Selection ◽  
Cell Receptor ◽  
Nkt Cells ◽  
Evolutionary Patterns ◽  
Mait Cells ◽  
Mhc Genes ◽  
Class 1 ◽  
Complementarity Determining Regions

Whereas major histocompatibility class-1 (MH1) proteins present peptides to T cells displaying a large T-cell receptor (TR) repertoire, MH1Like proteins, such as CD1D and MR1, present glycolipids and microbial riboflavin precursor derivatives, respectively, to T cells expressing invariant TR-α (iTRA) chains. The groove of such MH1Like, as well as iTRA chains used by mucosal-associated invariant T (MAIT) and natural killer T (NKT) cells, respectively, may result from a coevolution under particular selection pressures. Herein, we investigated the evolutionary patterns of the iTRA of MAIT and NKT cells and restricting MH1Like proteins: MR1 appeared 170 Mya and is highly conserved across mammals, evolving more slowly than other MH1Like. It has been pseudogenized or independently lost three times in carnivores, the armadillo, and lagomorphs. The corresponding TRAV1 gene also evolved slowly and harbors highly conserved complementarity determining regions 1 and 2. TRAV1 is absent exclusively from species in which MR1 is lacking, suggesting that its loss released the purifying selection on MR1. In the rabbit, which has very few NKT and no MAIT cells, a previously unrecognized iTRA was identified by sequencing leukocyte RNA. This iTRA uses TRAV41, which is highly conserved across several groups of mammals. A rabbit MH1Like gene was found that appeared with mammals and is highly conserved. It was independently lost in a few groups in which MR1 is present, like primates and Muridae, illustrating compensatory emergences of new MH1Like/Invariant T-cell combinations during evolution. Deciphering their role is warranted to search similar effector functions in humans.

scholarly journals Comparative Transcriptome Analysis Reveals Molecular Defensive Mechanism of Arachis hypogaea in Response to Salt Stress

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Hao Zhang ◽  
Xiaobo Zhao ◽  
Quanxi Sun ◽  
Caixia Yan ◽  
Juan Wang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Arachis Hypogaea ◽  
Genetic Manipulation ◽  
Plant Production ◽  
Cell Periphery ◽  
Oxidoreductase Activity ◽  
The World ◽  
Cultivated Peanut ◽  
Young Leaves

Abiotic stresses comprise all nonliving factors, such as soil salinity, drought, extreme temperatures, and metal toxicity, posing a serious threat to agriculture and affecting the plant production around the world. Peanut (Arachis hypogaea L.) is one of the most important crops for vegetable oil, proteins, minerals, and vitamins in the world. Therefore, it is of importance to understand the molecular mechanism of peanut against salt stress. Six transcriptome sequencing libraries including 24-hour salt treatments and control samples were constructed from the young leaves of peanut. A comprehensive analysis between two groups detected 3,425 differentially expressed genes (DEGs) including 2,013 upregulated genes and 1,412 downregulated genes. Of these DEGs, 141 transcription factors (TFs) mainly consisting of MYB, AP2/ERF, WRKY, bHLH, and HSF were identified in response to salinity stress. Further, GO categories of the DEGs highly related to regulation of cell growth, cell periphery, sustained external encapsulating structure, cell wall organization or biogenesis, antioxidant activity, and peroxidase activity were significantly enriched for upregulated DEGs. The function of downregulated DEGs was mainly enriched in regulation of metabolic processes, oxidoreductase activity, and catalytic activity. Fourteen DEGs with response to salt tolerance were validated by real-time PCR. Taken together, the identification of DEGs’ response to salt tolerance of cultivated peanut will provide a solid foundation for improving salt-tolerant peanut genetic manipulation in the future.

scholarly journals Molecular Phylogenetics and Evolutionary Analysis of a Highly Recombinant Begomovirus, Cotton Leaf Curl Multan Virus and Associated Satellites

2021 ◽  
Author(s):  
Tahir Farooq ◽  
Muhammad Umar ◽  
Xiaoman She ◽  
Yafei Tang ◽  
Zifu He
Keyword(s):  
Molecular Phylogenetics ◽  
Management Strategies ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Cotton Leaf ◽  
Evolutionary Analysis ◽  
Cotton Production ◽  
Evolutionary Patterns ◽  
Satellite Sequences ◽  
Leaf Curl

Abstract Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite’s virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite (CLCuMuA) and Cotton leaf curl Multan betasatellite (CLCuMuB) populations arising from distinct regions exhibit high mutation rates. Though evolutionary linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.

scholarly journals Involvement of Root Hair during <i>Rhizobial</i> Invasion in Cultivated Peanut (<i>Arachis hypogaea</i> L.)

2018 ◽  
Vol 09 (08) ◽  
pp. 1646-1659
Author(s):  
James Maku ◽  
Liping Wang ◽  
Fengxia Liu ◽  
Lixia Liu ◽  
Karen Kelley ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Root Hair ◽  
Cultivated Peanut

scholarly journals Recombinants from the crosses between amphidiploid and cultivated peanut (Arachis hypogaea) for pest-resistance breeding programs

PLoS ONE ◽  
2017 ◽  
Vol 12 (4) ◽  
pp. e0175940 ◽  
Author(s):  
Ailton Ferreira de Paula ◽  
Naiana Barbosa Dinato ◽  
Bianca Baccili Zanotto Vigna ◽  
Alessandra Pereira Fávero
Keyword(s):  
Arachis Hypogaea ◽  
Pest Resistance ◽  
Resistance Breeding ◽  
Breeding Programs ◽  
Cultivated Peanut

An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations

2011 ◽  
Vol 124 (4) ◽  
pp. 653-664 ◽  
Author(s):  
Hongde Qin ◽  
Suping Feng ◽  
Charles Chen ◽  
Yufang Guo ◽  
Steven Knapp ◽  
...  
Keyword(s):  
Linkage Map ◽  
Arachis Hypogaea ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Arachis Hypogaea L ◽  
Cultivated Peanut

scholarly journals A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome

2010 ◽  
Vol 10 (1) ◽  
pp. 17 ◽  
Author(s):  
Yanbin Hong ◽  
Xiaoping Chen ◽  
Xuanqiang Liang ◽  
Haiyan Liu ◽  
Guiyuan Zhou ◽  
...  
Keyword(s):  
Linkage Map ◽  
Arachis Hypogaea ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Arachis Hypogaea L ◽  
Cultivated Peanut

scholarly journals Genetic Studies Involving Wine Testa Color in Peanut1

1997 ◽  
Vol 24 (1) ◽  
pp. 60-62 ◽  
Author(s):  
W. D. Branch
Keyword(s):  
Arachis Hypogaea ◽  
Genetic Study ◽  
Genetic Studies ◽  
Arachis Hypogaea L ◽  
True Breeding ◽  
Cultivated Peanut ◽  
Testa Color ◽  
New Cultivars

Abstract A better understanding of peanut (Arachis hypogaea L.) testa color genetics would be helpful to breeders in developing new cultivars to meet U.S. market acceptability. Wine is one of the least understood of all basic testa colors in peanut. The objective of this genetic study was to gain further knowledge on the inheritance of wine testa color and possible allelic interactions. Crosses were made using two true-breeding wine testa color genotypes (Wine-Frr and PI 264549) as females with the tan testa and recessive red testa male parents Krinkle-Leaf and Makulu Red, respectively. F1, F2, and F3 data suggest no difference between the two wine testa color genotypes. Inheritance of wine testa color was found to be recessive with a one gene difference between wine and the tan testa color of Krinkle-Leaf, and with two gene differences between wine and the recessive red testa color of Makulu Red. Inheritance of wine seems to closely parallel that for recessive red testa color in the cultivated peanut.

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