High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in Capsicum frutescens

Zhong, Yangmin; Cheng, Yuan; Ruan, Meiying; Ye, Qingjing; Wang, Rongqing; Yao, Zhen; Zhou, Guozhi; Liu, Jia; Yu, Jiahong; Wan, Hongjian

doi:10.3390/horticulturae7070187

Cited by 21 publications

(15 citation statements)

References 48 publications

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“…Due to these characteristics, they are the most widely recognized genetic markers actively used in plant breeding. SSR markers are widely utilized for a variety of purposes, including population genetics, functional diversity, linkage mapping, DNA fingerprinting, and most importantly, assisted breeding techniques [ 55 ]. A total of 931 numbers of hub gene sequences, which include both lncRNA and mRNA targets of miRNAs, were analyzed by the MISA tool.…”

Section: Resultsmentioning

confidence: 99%

Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis

Mishra

Majumdar

Kumar

et al. 2023

International Journal of Genomics

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Climate change has become a major source of concern, particularly in agriculture, because it has a significant impact on the production of economically important crops such as wheat, rice, and maize. In the present study, an attempt has been made to identify differentially expressed heat stress-responsive long non-coding RNAs (lncRNAs) in the wheat genome using publicly available wheat transcriptome data (24 SRAs) representing two conditions, namely, control and heat-stressed. A total of 10,965 lncRNAs have been identified and, among them, 153, 143, and 211 differentially expressed transcripts have been found under 0 DAT, 1 DAT, and 4 DAT heat-stress conditions, respectively. Target prediction analysis revealed that 4098 lncRNAs were targeted by 119 different miRNA responses to a plethora of environmental stresses, including heat stress. A total of 171 hub genes had 204 SSRs (simple sequence repeats), and a set of target sequences had SNP potential as well. Furthermore, gene ontology analysis revealed that the majority of the discovered lncRNAs are engaged in a variety of cellular and biological processes related to heat stress responses. Furthermore, the modeled three-dimensional (3D) structures of hub genes encoding proteins, which had an appropriate range of similarity with solved structures, provided information on their structural roles. The current study reveals many elements of gene expression regulation in wheat under heat stress, paving the way for the development of improved climate-resilient wheat cultivars.

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Section: Resultsmentioning

confidence: 99%

Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis

Mishra

Majumdar

Kumar

et al. 2023

International Journal of Genomics

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“…Similar to our findings, Duan et al [ 47 ] investigated genetic diversity in 149 Chinese fir using the same 20 SSR markers and found these markers with high H o, H e and I values. Having high genetic parameter values for a marker is a vital indicator that the marker can be successfully used for closely related species/cultivars authentication [ 48 ]. Therefore, we propose that these loci can serve as high-resolution makers in estimation of genetic diversity and identification of inbred lines of Chinese fir.…”

Section: Resultsmentioning

confidence: 99%

Inbreeding in Chinese Fir: Insight into the Rare Self-Fertilizing Event from a Genetic View

Huang

Zeng

Deng

et al. 2022

Genes

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Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a fast-growing conifer with great forestation value and prefers outcrossing with high inbreeding depression effect. Previously, we captured a special Chinese fir parent clone named as ‘cx569’ that lacks early inbreeding depression. In view of the fact that very little has been published about the rare self-fertilizing event in Chinese fir from a genetic view, herein, we conduct an SSR-based study on the variation of open- and self-pollinated offspring of this parent to gain a view of the rare self-fertilizing event. The results indicated that genetic diversity of self-pollinated offspring was significantly reduced by half (Ho: 0.302, vs. 0.595, p = 0.001; He: 0.274 vs. 0.512, p = 0.002) when compared to an open-pollinated set. Self-pollinated offspring also had significantly positive FIS values (FIS = 0.057, p = 0.034) with a much higher proportion of common allele (20.59% vs. 0), reflecting their heterozygote deficiency. Clustering analysis further indicated a separation of the self- and opened- pollinated groups, implying a natural preference of outcrossing for cx569. However, the cx569 still had 6% acceptance for selfing. When accepted 100% for its own pollen, the cx569 led to a genetically unique selfing group. Additionally, this selfing group seemed to be consistently homozygous at seven particular loci. These findings gave us more genetic clues to gain insight into the rare self-fertilizing event in conifer (Chinese fir).

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“…For New Mexican germplasm, the genetic diversity of chile pepper landraces from Northern New Mexico was evaluated using random amplified polymorphic DNA ( Votava et al, 2005 ) and it was observed that the Northern New Mexico cultivars were more closely related to the Mexican varieties than the Southern New Mexican cultivars. Simple sequence repeat (SSR) markers characterized the genetic diversity of 147 C. frutescens accessions from 25 countries and clustered the population into seven major groups consistent with their geographic origins ( Zhong et al, 2021 ). In another study, SSR marker-based genetic diversity of 32 Phytophthora capsici resistant accessions of C. annuum from Ethiopia and India were evaluated and the genotypes clustered into three genetic resistance groups ( Rabuma et al, 2020 ).…”

Section: Gene Bank Collections and Genetic Diversitymentioning

confidence: 99%

Chile Pepper (Capsicum) Breeding and Improvement in the “Multi-Omics” Era

et al. 2022

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Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have “defined” the state of New Mexico, USA. The official state question, “Red or Green?” refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in “multi-omics,” that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.

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High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in Capsicum frutescens

Cited by 21 publications

References 48 publications

Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis

Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis

Inbreeding in Chinese Fir: Insight into the Rare Self-Fertilizing Event from a Genetic View

Chile Pepper (Capsicum) Breeding and Improvement in the “Multi-Omics” Era

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