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Peanut Genetic Breeding and Germplasm Innovation
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Peanut Genetic Breeding and Germplasm Innovation

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 February 2024) | Viewed by 6910

Special Issue Editor

Dr. Shuzhen Zhao

E-Mail Website
Guest Editor
Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
Interests: peanut resistance and peanut molecular breeding

Special Issue Information

Dear Colleagues,

This Special Issue on “Peanut Genetic Breeding and Germplasm Innovation” is dedicated to providing readers with cutting-edge information on transgenic breeding and marker-assisted breeding in peanut. Our primary focus is on publishing both fundamental and applied studies in the areas of molecular genetic breeding principles, molecular breeding techniques, molecular breeding research trends, and breeding for elite germplasm in the peanut breeding sector. All published research papers should cover the latest research with innovative significance, especially in the field of peanut breeding, including transgenic research, QTL analysis, genome-wide association analysis, genetic diversity of germplasm resources, and genetic breeding. In addition to plant geneticists and plant breeders, the readers of this Special Issue will primarily consist of specialists in the research, development, and marketing of peanut seeds.

Dr. Shuzhen Zhao
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • transgenic research
  • QTL analysis
  • genome-wide association analysis
  • genetic diversity of germplasm resources
  • genetic breeding

Published Papers (5 papers)

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Research

14 pages, 4204 KiB  
Article
Genome-Wide Characterization of the Phenylalanine Ammonia-Lyase Gene Family and Their Potential Roles in Response to Aspergillus flavus L. Infection in Cultivated Peanut (Arachis hypogaea L.)
by Pengpei Chai, Mengjie Cui, Qi Zhao, Linjie Chen, Tengda Guo, Jingkun Guo, Chendi Wu, Pei Du, Hua Liu, Jing Xu, Zheng Zheng, Bingyan Huang, Wenzhao Dong, Suoyi Han and Xinyou Zhang
Genes 2024, 15(3), 265; https://doi.org/10.3390/genes15030265 - 21 Feb 2024
Viewed by 1219
Abstract
Phenylalanine ammonia-lyase (PAL) is an essential enzyme in the phenylpropanoid pathway, in which numerous aromatic intermediate metabolites play significant roles in plant growth, adaptation, and disease resistance. Cultivated peanuts are highly susceptible to Aspergillus flavus L. infection. Although PAL genes have been characterized [...] Read more.
Phenylalanine ammonia-lyase (PAL) is an essential enzyme in the phenylpropanoid pathway, in which numerous aromatic intermediate metabolites play significant roles in plant growth, adaptation, and disease resistance. Cultivated peanuts are highly susceptible to Aspergillus flavus L. infection. Although PAL genes have been characterized in various major crops, no systematic studies have been conducted in cultivated peanuts, especially in response to A. flavus infection. In the present study, a systematic genome-wide analysis was conducted to identify PAL genes in the Arachis hypogaea L. genome. Ten AhPAL genes were distributed unevenly on nine A. hypogaea chromosomes. Based on phylogenetic analysis, the AhPAL proteins were classified into three groups. Structural and conserved motif analysis of PAL genes in A. hypogaea revealed that all peanut PAL genes contained one intron and ten motifs in the conserved domains. Furthermore, synteny analysis indicated that the ten AhPAL genes could be categorized into five pairs and that each AhPAL gene had a homologous gene in the wild-type peanut. Cis-element analysis revealed that the promoter region of the AhPAL gene family was rich in stress- and hormone-related elements. Expression analysis indicated that genes from Group I (AhPAL1 and AhPAL2), which had large number of ABRE, WUN, and ARE elements in the promoter, played a strong role in response to A. flavus stress. Full article
(This article belongs to the Special Issue Peanut Genetic Breeding and Germplasm Innovation)
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12 pages, 4372 KiB  
Article
Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (Arachis hypogaea L.)
by Dandan Luo, Lei Shi, Ziqi Sun, Feiyan Qi, Hongfei Liu, Lulu Xue, Xiaona Li, Han Liu, Pengyu Qu, Huanhuan Zhao, Xiaodong Dai, Wenzhao Dong, Zheng Zheng, Bingyan Huang, Liuyang Fu and Xinyou Zhang
Genes 2024, 15(2), 160; https://doi.org/10.3390/genes15020160 - 26 Jan 2024
Viewed by 1090
Abstract
The capability of embryogenic callus induction is a prerequisite for in vitro plant regeneration. However, embryogenic callus induction is strongly genotype-dependent, thus hindering the development of in vitro plant genetic engineering technology. In this study, to examine the genetic variation in embryogenic callus [...] Read more.
The capability of embryogenic callus induction is a prerequisite for in vitro plant regeneration. However, embryogenic callus induction is strongly genotype-dependent, thus hindering the development of in vitro plant genetic engineering technology. In this study, to examine the genetic variation in embryogenic callus induction rate (CIR) in peanut (Arachis hypogaea L.) at the seventh, eighth, and ninth subcultures (T7, T8, and T9, respectively), we performed genome-wide association studies (GWAS) for CIR in a population of 353 peanut accessions. The coefficient of variation of CIR among the genotypes was high in the T7, T8, and T9 subcultures (33.06%, 34.18%, and 35.54%, respectively), and the average CIR ranged from 1.58 to 1.66. A total of 53 significant single-nucleotide polymorphisms (SNPs) were detected (based on the threshold value −log10(p) = 4.5). Among these SNPs, SNPB03-83801701 showed high phenotypic variance and neared a gene that encodes a peroxisomal ABC transporter 1. SNPA05-94095749, representing a nonsynonymous mutation, was located in the Arahy.MIX90M locus (encoding an auxin response factor 19 protein) at T8, which was associated with callus formation. These results provide guidance for future elucidation of the regulatory mechanism of embryogenic callus induction in peanut. Full article
(This article belongs to the Special Issue Peanut Genetic Breeding and Germplasm Innovation)
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22 pages, 36382 KiB  
Article
Phylogenomic Analysis of Cytochrome P450 Gene Superfamily and Their Association with Flavonoids Biosynthesis in Peanut (Arachis hypogaea L.)
by Kun Zhang, Yongmei Qin, Wei Sun, Hourui Shi, Shuzhen Zhao, Liangqiong He, Changsheng Li, Jin Zhao, Jiaowen Pan, Guanghao Wang, Zhuqiang Han, Chuanzhi Zhao and Xiangli Yang
Genes 2023, 14(10), 1944; https://doi.org/10.3390/genes14101944 - 15 Oct 2023
Cited by 1 | Viewed by 1432
Abstract
Cytochrome P450s (CYPs) constitute extensive enzyme superfamilies in the plants, playing pivotal roles in a multitude of biosynthetic and detoxification pathways essential for growth and development, such as the flavonoid biosynthesis pathway. However, CYPs have not yet been systematically studied in the cultivated [...] Read more.
Cytochrome P450s (CYPs) constitute extensive enzyme superfamilies in the plants, playing pivotal roles in a multitude of biosynthetic and detoxification pathways essential for growth and development, such as the flavonoid biosynthesis pathway. However, CYPs have not yet been systematically studied in the cultivated peanuts (Arachis hypogaea L.), a globally significant cash crop. This study addresses this knowledge deficit through a comprehensive genome-wide analysis, leading to the identification of 589 AhCYP genes in peanuts. Through phylogenetic analysis, all AhCYPs were systematically classified into 9 clans, 43 gene families. The variability in the number of gene family members suggests specialization in biological functions. Intriguingly, both tandem duplication and fragment duplication events have emerged as pivotal drivers in the evolutionary expansion of the AhCYP superfamily. Ka/Ks analysis underscored the substantial influence of strong purifying selection on the evolution of AhCYPs. Furthermore, we selected 21 genes encoding 8 enzymes associated with the flavonoid pathway. The results of quantitative real-time PCR (qRT-PCR) experiments unveiled stage-specific expression patterns during the development of peanut testa, with discernible variations between pink and red testa. Importantly, we identified a direct correlation between gene expression levels and the accumulation of metabolites. These findings offer valuable insights into elucidating the comprehensive functions of AhCYPs and the underlying mechanisms governing the divergent accumulation of flavonoids in testa of different colors. Full article
(This article belongs to the Special Issue Peanut Genetic Breeding and Germplasm Innovation)
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16 pages, 1916 KiB  
Article
Mapping Quantitative Trait Loci (QTLs) for Hundred-Pod and Hundred-Seed Weight under Seven Environments in a Recombinant Inbred Line Population of Cultivated Peanut (Arachis hypogaea L.)
by Penghui Miao, Xinhao Meng, Zeren Li, Sainan Sun, Charles Y. Chen and Xinlei Yang
Genes 2023, 14(9), 1792; https://doi.org/10.3390/genes14091792 - 13 Sep 2023
Cited by 2 | Viewed by 1202
Abstract
The cultivated peanut (Arachis hypogaea L.) is a significant oil and cash crop globally. Hundred-pod and -seed weight are important components for peanut yield. To unravel the genetic basis of hundred-pod weight (HPW) and hundred-seed weight (HSW), in the current study, a [...] Read more.
The cultivated peanut (Arachis hypogaea L.) is a significant oil and cash crop globally. Hundred-pod and -seed weight are important components for peanut yield. To unravel the genetic basis of hundred-pod weight (HPW) and hundred-seed weight (HSW), in the current study, a recombinant inbred line (RIL) population with 188 individuals was developed from a cross between JH5 (JH5, large pod and seed weight) and M130 (small pod and seed weight), and was utilized to identify QTLs for HPW and HSW. An integrated genetic linkage map was constructed by using SSR, AhTE, SRAP, TRAP and SNP markers. This map consisted of 3130 genetic markers, which were assigned to 20 chromosomes, and covered 1998.95 cM with an average distance 0.64 cM. On this basis, 31 QTLs for HPW and HSW were located on seven chromosomes, with each QTL accounting for 3.7–10.8% of phenotypic variance explained (PVE). Among these, seven QTLs were detected under multiple environments, and two major QTLs were found on B04 and B08. Notably, a QTL hotspot on chromosome A08 contained seven QTLs over a 2.74 cM genetic interval with an 0.36 Mb physical map, including 18 candidate genes. Of these, Arahy.D52S1Z, Arahy.IBM9RL, Arahy.W18Y25, Arahy.CPLC2W and Arahy.14EF4H might play a role in modulating peanut pod and seed weight. These findings could facilitate further research into the genetic mechanisms influencing pod and seed weight in cultivated peanut. Full article
(This article belongs to the Special Issue Peanut Genetic Breeding and Germplasm Innovation)
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14 pages, 4290 KiB  
Article
Genome-Wide Identification and Characterization of the Phytochrome Gene Family in Peanut
by Yue Shen, Yonghui Liu, Man Liang, Xuyao Zhang, Zhide Chen and Yi Shen
Genes 2023, 14(7), 1478; https://doi.org/10.3390/genes14071478 - 20 Jul 2023
Viewed by 1384
Abstract
To investigate the potential role of phytochrome (PHY) in peanut growth and its response to environmental fluctuations, eight candidate AhPHY genes were identified via genome-wide analysis of cultivated peanut. These AhPHY polypeptides were determined to possess acidic and hydrophilic physiochemical properties and exhibit [...] Read more.
To investigate the potential role of phytochrome (PHY) in peanut growth and its response to environmental fluctuations, eight candidate AhPHY genes were identified via genome-wide analysis of cultivated peanut. These AhPHY polypeptides were determined to possess acidic and hydrophilic physiochemical properties and exhibit subcellular localization patterns consistent with residence in the nucleus and cytoplasm. Phylogenetic analysis revealed that the AhPHY gene family members were classified into three subgroups homologous to the PHYA/B/E progenitors of Arabidopsis. AhPHY genes within the same clade largely displayed analogous gene structure, conserved motifs, and phosphorylation sites. AhPHY exhibited symmetrical distribution across peanut chromosomes, with 7 intraspecific syntenic gene pairs in peanut, as well as 4 and 20 interspecific PHY syntenic gene pairs in Arabidopsis and soybean, respectively. A total of 42 cis-elements were predicted in AhPHY promoters, including elements implicated in phytohormone regulation, stress induction, physiology, and photoresponse, suggesting putative fundamental roles across diverse biological processes. Moreover, spatiotemporal transcript profiling of AhPHY genes in various peanut tissues revealed distinct expression patterns for each member, alluding to putative functional specialization. This study contributes novel insights into the classification, structure, molecular evolution, and expression profiles of the peanut phytochrome gene family, and also provides phototransduction gene resources for further mechanistic characterization. Full article
(This article belongs to the Special Issue Peanut Genetic Breeding and Germplasm Innovation)
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