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24 pages, 19496 KiB

Open AccessArticle

The Stilbene Synthase Family in Arachis: A Genome-Wide Study and Functional Characterization in Response to Stress

by Ana Cristina Miranda Brasileiro, Marcos Aparecido Gimenes, Bruna Medeiros Pereira, Ana Paula Zotta Mota, Matheus Nascimento Aguiar, Andressa Cunha Quintana Martins, Mario Alfredo Saraiva Passos and Patricia Messenberg Guimaraes

Genes 2023, 14(12), 2181; https://doi.org/10.3390/genes14122181 - 05 Dec 2023

Cited by 1 | Viewed by 951

Abstract

Peanut (Arachis hypogaea) and its wild relatives are among the few species that naturally synthesize resveratrol, a well-known stilbenoid phytoalexin that plays a crucial role in plant defense against biotic and abiotic stresses. Resveratrol has received considerable attention due to its [...] Read more.

Peanut (Arachis hypogaea) and its wild relatives are among the few species that naturally synthesize resveratrol, a well-known stilbenoid phytoalexin that plays a crucial role in plant defense against biotic and abiotic stresses. Resveratrol has received considerable attention due to its health benefits, such as preventing and treating various human diseases and disorders. Chalcone (CHS) and Stilbene (STS) Synthases are plant-specific type III Polyketide Synthases (PKSs) that share the same substrates and are key branch enzymes in the biosynthesis of flavonoids and stilbenoids, respectively. Although resveratrol accumulation in response to external stimulus has been described in peanut, there are no comprehensive studies of the CHS and STS gene families in the genus Arachis. In the present study, we identified and characterized 6 CHS and 46 STS genes in the tetraploid peanut and an average of 4 CHS and 22 STS genes in three diploid wild species (Arachis duranensis, Arachis ipaënsis and Arachis stenosperma). The CHS and STS gene and protein structures, chromosomal distributions, phylogenetic relationships, conserved amino acid domains, and cis-acting elements in the promoter regions were described for all Arachis species studied. Based on gene expression patterns of wild A. stenosperma STS genes in response to different biotic and abiotic stresses, we selected the candidate AsSTS4 gene, which is strongly induced by ultraviolet (UV) light exposure, for further functional investigation. The AsSTS4 overexpression in peanut hairy roots significantly reduced (47%) root-knot nematode infection, confirming that stilbene synthesis activation in transgenic plants can increase resistance to pathogens. These findings contribute to understanding the role of resveratrol in stress responses in Arachis species and provide the basis for genetic engineering for improved production of valuable secondary metabolites in plants. Full article

(This article belongs to the Special Issue Peanut Genetics and Omics)

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13 pages, 4384 KiB

Open AccessArticle

Dissection of the Genetic Basis of Resistance to Stem Rot in Cultivated Peanuts (Arachis hypogaea L.) through Genome-Wide Association Study

by Liying Yan, Wanduo Song, Zhihui Wang, Dongyang Yu, Hari Sudini, Yanping Kang, Yong Lei, Dongxin Huai, Yuning Chen, Xin Wang, Qianqian Wang and Boshou Liao

Genes 2023, 14(7), 1447; https://doi.org/10.3390/genes14071447 - 14 Jul 2023

Cited by 1 | Viewed by 1055

Abstract

Peanut (Arachis hypogaea) is an important oilseed and cash crop worldwide, contributing an important source of edible oil and protein for human nutrition. However, the incidence of stem rot disease caused by Athelia rolfsii poses a major challenge to peanut cultivation, [...] Read more.

Peanut (Arachis hypogaea) is an important oilseed and cash crop worldwide, contributing an important source of edible oil and protein for human nutrition. However, the incidence of stem rot disease caused by Athelia rolfsii poses a major challenge to peanut cultivation, resulting in significant yield losses. In this study, a panel of 202 peanut accessions was evaluated for their resistance to stem rot by inoculating plants in the field with A. rolfsii-infested oat grains in three environments. The mean disease index value of each environment for accessions in subsp. fasitigiate and subsp. hypogaea showed no significant difference. Accessions from southern China displayed the lowest disease index value compared to those from other ecological regions. We used whole-genome resequencing to analyze the genotypes of the accessions and to identify significant SNPs associated with stem rot resistance through genome-wide association study (GWAS). A total of 121 significant SNPs associated with stem rot resistance in peanut were identified, with phenotypic variation explained (PVE) ranging from 12.23% to 15.51%. A total of 27 candidate genes within 100 kb upstream and downstream of 23 significant SNPs were annotated, which have functions related to recognition, signal transduction, and defense response. These significant SNPs and candidate genes provide valuable information for further validation and molecular breeding to improve stem rot resistance in peanut. Full article

(This article belongs to the Special Issue Peanut Genetics and Omics)

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20 pages, 2577 KiB

Open AccessArticle

Mapping of QTLs Associated with Biological Nitrogen Fixation Traits in Peanuts (Arachis hypogaea L.) Using an Interspecific Population Derived from the Cross between the Cultivated Species and Its Wild Ancestors

by Darius T. Nzepang, Djamel Gully, Joël R. Nguepjop, Arlette Zaiya Zazou, Hodo-Abalo Tossim, Aissatou Sambou, Jean-François Rami, Valerie Hocher, Saliou Fall, Sergio Svistoonoff and Daniel Fonceka

Genes 2023, 14(4), 797; https://doi.org/10.3390/genes14040797 - 26 Mar 2023

Viewed by 1332

Abstract

Peanuts (Arachis hypogaea L.) are an allotetraploid grain legume mainly cultivated by poor farmers in Africa, in degraded soil and with low input systems. Further understanding nodulation genetic mechanisms could be a relevant option to facilitate the improvement of yield and lift [...] Read more.

Peanuts (Arachis hypogaea L.) are an allotetraploid grain legume mainly cultivated by poor farmers in Africa, in degraded soil and with low input systems. Further understanding nodulation genetic mechanisms could be a relevant option to facilitate the improvement of yield and lift up soil without synthetic fertilizers. We used a subset of 83 chromosome segment substitution lines (CSSLs) derived from the cross between a wild synthetic tetraploid AiAd (Arachis ipaensis × Arachis duranensis)^4× and the cultivated variety Fleur11, and evaluated them for traits related to BNF under shade-house conditions. Three treatments were tested: without nitrogen; with nitrogen; and without nitrogen, but with added0 Bradyrhizobium vignae strain ISRA400. The leaf chlorophyll content and total biomass were used as surrogate traits for BNF. We found significant variations for both traits specially linked to BNF, and four QTLs (quantitative trait loci) were consistently mapped. At all QTLs, the wild alleles decreased the value of the trait, indicating a negative effect on BNF. A detailed characterization of the lines carrying those QTLs in controlled conditions showed that the QTLs affected the nitrogen fixation efficiency, nodule colonization, and development. Our results provide new insights into peanut nodulation mechanisms and could be used to target BNF traits in peanut breeding programs. Full article

(This article belongs to the Special Issue Peanut Genetics and Omics)

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13 pages, 1813 KiB

Open AccessArticle

Identification and Pyramiding Major QTL Loci for Simultaneously Enhancing Aflatoxin Resistance and Yield Components in Peanut

by Gaorui Jin, Nian Liu, Bolun Yu, Yifei Jiang, Huaiyong Luo, Li Huang, Xiaojing Zhou, Liying Yan, Yanping Kang, Dongxin Huai, Yinbing Ding, Yuning Chen, Xin Wang, Huifang Jiang, Yong Lei, Jinxiong Shen and Boshou Liao

Genes 2023, 14(3), 625; https://doi.org/10.3390/genes14030625 - 01 Mar 2023

Cited by 1 | Viewed by 1392

Abstract

Peanut is susceptible to Aspergillus flavus infection, and the consequent aflatoxin contamination has been recognized as an important risk factor affecting food safety and industry development. Planting peanut varieties with resistance to aflatoxin contamination is regarded as an ideal approach to decrease the [...] Read more.

Peanut is susceptible to Aspergillus flavus infection, and the consequent aflatoxin contamination has been recognized as an important risk factor affecting food safety and industry development. Planting peanut varieties with resistance to aflatoxin contamination is regarded as an ideal approach to decrease the risk in food safety, but most of the available resistant varieties have not been extensively used in production because of their low yield potential mostly due to possessing small pods and seeds. Hence, it is highly necessary to integrate resistance to aflatoxin and large seed weight. In this study, an RIL population derived from a cross between Zhonghua 16 with high yield and J 11 with resistance to infection of A. flavus and aflatoxin production, was used to identify quantitative trait locus (QTL) for aflatoxin production (AP) resistance and hundred-seed weight (HSW). From combined analysis using a high-density genetic linkage map constructed, 11 QTLs for AP resistance with 4.61–11.42% phenotypic variation explanation (PVE) and six QTLs for HSW with 3.20–28.48% PVE were identified, including three major QTLs for AP resistance (qAFTA05.1, qAFTB05.2 and qAFTB06.3) and three for HSW (qHSWA05, qHSWA08 and qHSWB06). In addition, qAFTA05.1, qAFTB06.3, qHSWA05, qHSWA08 and qHSWB06 were detected in multiple environments. The aflatoxin contents under artificial inoculation were decreased by 34.77–47.67% in those segregated lines harboring qAFTA05.1, qAFTB05.2 and qAFTB06.3, while the HSWs were increased by 47.56–49.46 g in other lines harboring qHSWA05, qHSWA08 and qHSWB06. Conditional QTL mapping indicated that HSW and percent seed infection index (PSII) had no significant influence on aflatoxin content. Interestingly, the QT 1059 simultaneously harboring alleles of aflatoxin content including qAFTA05.1 and qAFTB05.2, alleles of PSII including qPSIIB03.1, qPSIIB03.2, and qPSIIB10 and alleles of HSW including qHSWA05, qHSWB06, qHSWA08 had better resistance to A. flavus infection and to toxin production and higher yield potential compared with the two parents of the RIL. The above identified major loci for AP resistance and HWS would be helpful for marker-assisted selection in peanut breeding. Full article

(This article belongs to the Special Issue Peanut Genetics and Omics)

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16 pages, 4354 KiB

Open AccessArticle

Root Metabolism and Effects of Root Exudates on the Growth of Ralstonia solanacearum and Fusarium moniliforme Were Significantly Different between the Two Genotypes of Peanuts

by Zhong Li, Wenfeng Guo, Changming Mo, Ronghua Tang, Liangqiong He, Lin Du, Ming Li, Haining Wu, Xiumei Tang, Zhipeng Huang and Xingjian Wu

Genes 2023, 14(2), 528; https://doi.org/10.3390/genes14020528 - 20 Feb 2023

Cited by 3 | Viewed by 1821

Abstract

Wild peanut species Arachis correntina (A. correntina) had a higher continuous cropping tolerance than peanut cultivars, closely correlating with the regulatory effects of its root exudates on soil microorganisms. To reveal the resistance mechanism of A. correntina to pathogens, we adopted transcriptomic [...] Read more.

Wild peanut species Arachis correntina (A. correntina) had a higher continuous cropping tolerance than peanut cultivars, closely correlating with the regulatory effects of its root exudates on soil microorganisms. To reveal the resistance mechanism of A. correntina to pathogens, we adopted transcriptomic and metabolomics approaches to analyze differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) between A. correntina and peanut cultivar Guihua85 (GH85) under hydroponic conditions. Interaction experiments of peanut root exudates with Ralstonia solanacearum (R. solanacearum) and Fusarium moniliforme (F. moniliforme) were carried out in this study. The result of transcriptome and metabolomics association analysis showed that there were fewer up-regulated DEGs and DEMs in A. correntina compared with GH85, which were closely associated with the metabolism of amino acids and phenolic acids. Root exudates of GH85 had stronger effects on promoting the growth of R. solanacearum and F. moniliforme than those of A. correntina under 1 and 5 percent volume (1% and 5%) of root exudates treatments. Thirty percent volume (30%) of A. correntina and GH85 root exudates significantly inhibited the growth of two pathogens. The exogenous amino acids and phenolic acids influenced R. solanacearum and F. moniliforme showing concentration effects from growth promotion to inhibition as with the root exudates. In conclusion, the greater resilience of A. correntina) to changes in metabolic pathways for amino acids and phenolic acids might aid in the repression of pathogenic bacteria and fungi. Full article

(This article belongs to the Special Issue Peanut Genetics and Omics)

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13 pages, 2495 KiB

Open AccessArticle

Insights into the Novel FAD2 Gene Regulating Oleic Acid Accumulation in Peanut Seeds with Different Maturity

by Shuzhen Zhao, Jie Sun, Jinbo Sun, Xiaoqian Zhang, Chuanzhi Zhao, Jiaowen Pan, Lei Hou, Ruizheng Tian and Xingjun Wang

Genes 2022, 13(11), 2076; https://doi.org/10.3390/genes13112076 - 09 Nov 2022

Cited by 4 | Viewed by 2022

Abstract

AhFAD2 is a key enzyme catalyzing the conversion of oleic acid into linoleic acid. The high oleic acid characteristic of peanut mainly comes from the homozygous recessive mutation of AhFAD2A and AhFAD2B genes (aabb). However, even in high-oleic-acid varieties with the aabb genotype, [...] Read more.

AhFAD2 is a key enzyme catalyzing the conversion of oleic acid into linoleic acid. The high oleic acid characteristic of peanut mainly comes from the homozygous recessive mutation of AhFAD2A and AhFAD2B genes (aabb). However, even in high-oleic-acid varieties with the aabb genotype, the oleic acid content of seeds with different maturity varies significantly. Therefore, in addition to AhFAD2A and AhFAD2B, other FAD2 members or regulators may be involved in this process. Which FAD2 genes are involved in the regulatory processes associated with seed maturity is still unclear. In this study, four stable lines with different genotypes (AABB, aaBB, AAbb, and aabb) were used to analyze the contents of oleic acid and linoleic acid at different stages of seed development in peanut. Three new AhFAD2 genes (AhFAD2–7, AhFAD2–8, and AhFAD2–9) were cloned based on the whole-genome sequencing results of cultivated peanuts. All peanut FAD2 genes showed tissue preference in expression; however, only the expression level of AhFAD2-7 was positively correlated with the linoleic acid concentration in peanut seeds. These findings provide new insights into the regulation of oleic acid accumulation by maturity, and AhFAD2-7 plays an important role in the maturity dependent accumulation of oleic acid and linoleic acid in peanut. Full article

(This article belongs to the Special Issue Peanut Genetics and Omics)

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15 pages, 2452 KiB

Open AccessArticle

Transcriptomic Analysis Provides Insights into the Differential Effects of Aluminum on Peanut (Arachis hypogaea L.)

by Gegen Bao, Shengyu Li, Qi Zhou, Umair Ashraf, Jingxuan Qiao, Xiaolin Li, Xiaorong Wan and Yixiong Zheng

Genes 2022, 13(10), 1830; https://doi.org/10.3390/genes13101830 - 10 Oct 2022

Cited by 4 | Viewed by 1425

Abstract

In acidic soils, high concentrations of aluminum ions (Al³⁺) in dissolved form reduce root growth and development of most crops. In addition, Al³⁺ is also a beneficial element in some plant species in low concentrations. However, the regulatory mechanism of [...] Read more.

In acidic soils, high concentrations of aluminum ions (Al³⁺) in dissolved form reduce root growth and development of most crops. In addition, Al³⁺ is also a beneficial element in some plant species in low concentrations. However, the regulatory mechanism of the growth and development of peanut (Arachis hypogaea L.) treated with different concentrations of Al³⁺ has been rarely studied. In this study, peanut seedlings were treated with AlCl₃.18H₂O in Hoagland nutrient solution at four different concentrations of Al^3+, i.e., 0 (pH 6.85), 1.25 (pH 4.03), 2.5 (pH 3.85), and 5 (pH 3.69) mmol/L, which are regarded as Al0, Al1, Al2, and Al3. The results showed that low concentrations of Al treatment (Al1) promoted peanut growth, while high concentrations of Al treatments (Al2 and Al3) significantly inhibited peanut growth. Compared with the control (Al0), transcriptome analysis showed that the differentially expressed genes (DEGs) of starch and sucrose metabolic pathways were significantly enriched at low concentrations, i.e., Al1 treatment, whereas the expression of AhERD6 (sugar transporter) was significantly up-regulated, and the soluble sugar content was significantly increased. The DEGs of the plant hormone signaling transduction pathway were significantly enriched at high concentrations of Al2 and Al3 treatments, whereas the expression of AhNCED1 (9-cis-epoxycarotenoid dioxygenase) was significantly up-regulated, and the content of ABA was significantly increased. Moreover, the expression of transcription factors (TFs) in peanut was affected by different concentrations of Al. Overall, low concentrations of Al1 promoted peanut growth by increasing soluble sugar content, while high concentrations of Al2 and Al3 inhibited the growth of peanut, induced AhNCED1 gene expression, and increased endogenous ABA content. For peanut, the exposure of Al at low concentrations not only derived an adaptive mechanism to cope with Al stress, but also acted as a stimulator to promote its growth and development. Full article

(This article belongs to the Special Issue Peanut Genetics and Omics)

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Review

Jump to: Research

23 pages, 1201 KiB

Open AccessReview

An Overview of Mapping Quantitative Trait Loci in Peanut (Arachis hypogaea L.)

by Fentanesh C. Kassie, Joël R. Nguepjop, Hermine B. Ngalle, Dekoum V. M. Assaha, Mesfin K. Gessese, Wosene G. Abtew, Hodo-Abalo Tossim, Aissatou Sambou, Maguette Seye, Jean-François Rami, Daniel Fonceka and Joseph M. Bell

Genes 2023, 14(6), 1176; https://doi.org/10.3390/genes14061176 - 28 May 2023

Cited by 1 | Viewed by 2088

Abstract

Quantitative Trait Loci (QTL) mapping has been thoroughly used in peanut genetics and breeding in spite of the narrow genetic diversity and the segmental tetraploid nature of the cultivated species. QTL mapping is helpful for identifying the genomic regions that contribute to traits, [...] Read more.

Quantitative Trait Loci (QTL) mapping has been thoroughly used in peanut genetics and breeding in spite of the narrow genetic diversity and the segmental tetraploid nature of the cultivated species. QTL mapping is helpful for identifying the genomic regions that contribute to traits, for estimating the extent of variation and the genetic action (i.e., additive, dominant, or epistatic) underlying this variation, and for pinpointing genetic correlations between traits. The aim of this paper is to review the recently published studies on QTL mapping with a particular emphasis on mapping populations used as well as traits related to kernel quality. We found that several populations have been used for QTL mapping including interspecific populations developed from crosses between synthetic tetraploids and elite varieties. Those populations allowed the broadening of the genetic base of cultivated peanut and helped with the mapping of QTL and identifying beneficial wild alleles for economically important traits. Furthermore, only a few studies reported QTL related to kernel quality. The main quality traits for which QTL have been mapped include oil and protein content as well as fatty acid compositions. QTL for other agronomic traits have also been reported. Among the 1261 QTL reported in this review, and extracted from the most relevant studies on QTL mapping in peanut, 413 (~33%) were related to kernel quality showing the importance of quality in peanut genetics and breeding. Exploiting the QTL information could accelerate breeding to develop highly nutritious superior cultivars in the face of climate change. Full article

(This article belongs to the Special Issue Peanut Genetics and Omics)

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