Farmers’ Perceptions of Pepper Genetic Diversity in Niger | IJAAR 2025

Halimatou Ousseini Maiga, from the Faculty of Agronomy, Abdou Moumouni University of Niamey, Niger. Oumarou Souleymane, from the National Institute of Agronomic Research of Niger, Niamey, Niger.  Illiassou Mossi Maiga, from the National Institute of Agronomic Research of Niger, Niamey, Niger.    Adam Toudou, from the Faculty of Agronomy, Abdou Moumouni University of Niamey, Niger. Wrote a research article about, Farmers’ Perceptions of Pepper Genetic Diversity in Niger. Entitled, Farmers perception of the genetic diversity of peppers (Capsicum annuum) in Niger: Between tradition and innovation. This research paper published by the International Journal of Agronomy and AgriculturalResearch | IJAAR. an open access scholarly research journal on Agricultural Research.  under the affiliation of the International Network For Natural Sciences| INNSpub. an open access multidisciplinary research journal publisher.

Abstract

Genetic diversity plays a crucial role in crop development on farms facing the growing challenges posed by climate change. Rural bell pepper growers in Niger are heavily dependent on this biodiversity, for which they are constantly seeking a balance to ensure sustainable production. Studying farmers’ perceptions of bell pepper genetic diversity in Niger is a necessity to explore the relationship between traditional farming practices and innovative approaches to crop diversity management.  The aim of this study is to understand how farmers in Niger perceive and use bell pepper genetic diversity. To this end, a survey was carried out in the country’s main pepper-growing regions. The results showed the existence of a great diversity of accessions, the use of rich and varied farmer descriptors and the coexistence of 3 systems: traditional, improved and a combination of the two. In addition, the study showed that several factors influence farmers’ choices and preferences in the selection of bell pepper accessions, as well as the seed system used. 

Introduction

Pepper (Capsicum annuum L.), a member of the Solanaceae family, originates from Mexico, with Guatemala identified as its secondary center of origin (Bukasov, 1930). The most widely cultivated species, C. annuum (2n = 2x = 24), possesses a genome size of 3.48 GB (Kim et al., 2014). It is a predominantly selfpollinated crop, although the cross-pollination rate can reach up to 10% (Rai et al., 2013). Pepper is a major horticultural crop with substantial commercial importance and medicinal value. Globally, approximately 36 million tons of peppers are produced on about 2 million hectares. China is the leading producer, accounting for 46% of global production, followed by Mexico, Indonesia, and Turkey (FAO, 2021). Genetic diversity plays a pivotal role in the development of climate-resilient crops, particularly in the context of the increasing challenges posed by climate change. Within the broader framework of agricultural adaptation, the conservation and utilization of genetic diversity represent key strategies to enhance agricultural resilience (Mohamed et al., 2025). Moreover, genetic diversity is fundamental to both natural evolutionary processes and breeding programs. Through genetic variation, crop species are able to survive and adapt to diverse and changing environmental conditions (Salgotra and Chauhan, 2023).

In Niger, pepper (Capsicum annuum L.) is a key crop, highly valued for its economic importance as well as its cultural significance. However, increasing environmental pressures, the evolution of agricultural systems, and shifting market demands have compelled farmers to continuously adapt their cultivation strategies. Understanding farmers‘ perceptions of genetic diversity in pepper has therefore become crucial for exploring the complex relationship between traditional agricultural practices and innovative approaches to crop diversity management. Such an investigation provides insight into how local knowledge systems evolve and integrate with modern agricultural innovations in response to changing socio-economic and environmental conditions. The present study aims to analyze how Nigerien farmers perceive, maintain, and utilize the genetic diversity of pepper. It seeks to identify the balance between time tested traditional knowledge and the potential offered by improved and emerging agricultural practices, contributing to the sustainable management and enhancement of pepper genetic resources in Niger.

Reference

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Article source : Farmers perception of the genetic diversity of peppers (Capsicum annuum) in Niger: Between traditionand innovation 

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Genetic Diversity of Omicron Spike Variants in Vietnam | IJB 2022

Quan Ke Thai, Department of Saigon University, 273 An Duong Vuong, Ward 3 District 5, Ho Chi Minh city, Vietnam. Phuoc Huynh, department of aVNU HCMC University of Science, 227 Nguyen Van Cu, Ward 4 District 5, Ho Chi Minh city, Vietnam. Yen Le Thi, department of DSI1191, Saigon University, 273 An Duong Vuong, Ward 3 District 5, Ho Chi Minh city, Vietnam.  Huyen Nguyen Thi Thuong, department of Biology, HCMC University of Education, 280 An Duong Vuong Ward 4 District 5, Ho Chi Minh city, Vietnam. Wrote a research article about, Genetic Diversity of Omicron Spike Variants in Vietnam. Entitled, Genetic diversity of SARS-CoV-2 Omicron variants’ spike gene in Vietnam. This research paper published by the International Journal of Biosciences | IJB. an open access scholarly research journal on Biosciences. under the affiliation of the International Network For Natural Sciences| INNSpub. an open access multidisciplinary research journal publisher.

Abstract

The recently emerging Omicron is of prime concern because this variant has been the cause of current large outbreaks. Omicron becomes more dangerous when numerous content mutations in the Spike (S) gene lead to more than 30 substitutions of amino acids in spike protein. Omicron variant had been identified as Variants Of Concern (VOC) when it had transmission rate overtake previous VOCs. In this report, we focus on analyzing the genetic diversity of the S gene of Omicron variants in Vietnam. Our results indicate the high level of haplotype diversity when confirmed 362 haplotypes and the haplotype diversity index at 0.9160 ± 0.0037. The analysis of nucleotide diversity display nucleotide diversity at 0.0053 ± 0.0026 and recorded 318 polymorphic sites with the average number of mutations of 40 ± 9. Almost missense mutations appeared in the RBD region, and deletion and insertion occurred in the NTD region. Besides, we note conserved mutation in the S gene of Omicron in Vietnam, namely C21618T G21987A T22200G G22578A C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G G22992A C22995A A23013C A23040G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A G23948T A24424T T24469A, and C25000T. Furthermore, the genetic networks of the S gene provided more correlation between infection and mutation in this gene. Ultimately, we propose the close relation between BA.2 and BA.4, BA.5 through the network, in which necessary focus T22917G (L452R), T23018G (F486V), and other novel mutations will appear in the S gene. The network provided the whole picture of Omicron variants in Vietnam, supporting the tracing of the source of a new outbreak in the future.  

Introduction

The recently emerging Omicron is of prime concern because this variant has been the cause of current large outbreaks. Omicron becomes more dangerous when numerous content mutations in the Spike (S) gene lead to more than 30 substitutions of amino acids in spike protein. Omicron variant had been identified as Variants Of Concern (VOC) when it had transmission rate overtake previous VOCs. In this report, we focus on analyzing the genetic diversity of the S gene of Omicron variants in Vietnam. Our results indicate the high level of haplotype diversity when confirmed 362 haplotypes and the haplotype diversity index at 0.9160 ± 0.0037. The analysis of nucleotide diversity display nucleotide diversity at 0.0053 ± 0.0026 and recorded 318 polymorphic sites with the average number of mutations of 40 ± 9. Almost missense mutations appeared in the RBD region, and deletion and insertion occurred in the NTD region. Besides, we note conserved mutation in the S gene of Omicron in Vietnam, namely C21618T G21987A T22200G G22578A C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G G22992A C22995A A23013C A23040G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A G23948T A24424T T24469A, and C25000T. Furthermore, the genetic networks of the S gene provided more correlation between infection and mutation in this gene. Ultimately, we propose the close relation between BA.2 and BA.4, BA.5 through the network, in which necessary focus T22917G (L452R), T23018G (F486V), and other novel mutations will appear in the S gene. The network provided the whole picture of Omicron variants in Vietnam, supporting the tracing of the source of a new outbreak in the future.

appearance of the Delta variant is almost eliminated, breaking the achievements preventing the pandemic in some countries. Delta's rapid transmission is determined mainly by the spike protein's L452R, T478K, and E484Q N501Y mutations (Kumar, Singh et al., 2021) (Fan, Hu et al., 2021). In addition, some substitutions, such as E484K, D614G, and P681H/R, have also been conserved in many different VOC variants (Papanikolaou, Chrysovergis et al., 2022) (Lubinski, Frazier et al., 2021) . Recently, a new variant is thought to be more infectious than the Delta variant and maintains from 30 to 45 mutations in the spike protein (Wei, Shan et al., 2021) (Kumar, Thambiraja et al., 2022). According to PANGO Lineages, this variant belongs to lineage B.1.1.529, named Omicron by WHO and classified as a VOC variant. Since December 2021, Omicron has almost replaced Delta as the primary source of infection infections in the United States (Fall, Eldesouki et al., 2022). After that, the Omicron variant became almost universally dominant and gradually replaced the previously dangerous Delta variant (Chaguza, Coppi et al., 2022).

Vietnam is one of the infrequent countries that has succeeded in controlling the epidemic situation in the early stages of the pandemic outbreak in the world. Vietnam has successfully gone 99 days with no community transmission, and most cases (60%) in Vietnam are due to entry from China, Europe, and the United States (Thai, Rabaa et al., 2021). Examination of genomics indicated that the nucleotide similarity of the sequences in Vietnam in the two outbreaks was very high (minimum 99.96%, mean 99.97%), combined with familiar mutation exhibiting that virus is not competent to silently infect the community from April 2020 (Phuong, Tung et al., 2021). In Vietnam, each epidemic wave corresponds to the emergence of a new variant with a more robust infectious fitness. During the third wave of epidemics (beginning on January 28, 2021), the outbreak in northern Vietnam occurred rapidly with the main contribution of Alpha variants (Chau, Hong et al., 2021). Then, the fourth wave (beginning on April 27, 2021) had been the worst ever experienced by the country. In May 2021, all patients in Vietnam were derived by the Delta variant (Nguyen, Wong et al., 2021). In November, this wave had caused 99.9% of total deaths in the country (Hoang, Pham et al., 2022). The Vietnamese government has had to implement unprecedented strict epidemic prevention measures, including encouraging people to isolate themselves at home, mobilizing the participation of the army and military medics, and setting up field hospitals. However, the epidemic situation had been still difficult to control because the Delta variant has high transmissibility.

After November 2021, when the vaccination rate in Vietnam reached a relatively high threshold, government took to restore social life under "new normal" conditions.

The gradual easing of epidemic prevention measures has facilitated the spread of the virus in the community. The first case confirmed that the Omicron variant was recorded in Vietnam on December 19, 2021. Until March 2022, the Omicron became the primary circulating variant and the cause of infections in the Hanoi capital. On March 12, 2022, Vietnam recorded the highest number of infections ever at 454,179 cases/day. This number is much larger than the previous wave of epidemics caused by the Delta variants. Proposes that Omicron will become the dominant variant in Vietnam shortly. Despite the sudden increase in cases, the mortality rate tends to be the opposite.

The number of deaths caused by the Omicron on March 13, 2022, is 95 cases, and the average of the last seven days is 82. These concerns were lower than Delta's 803 cases on September 1, 2021, and the average of the last seven days in 360 cases (according to Vietnam's Ministry of Health). The current research literature indicates that the Omicron variants are more infectious than previously recorded variants (Ren, Wang et al., 2022) (He, Hong et al., 2021). On the other hand, Omicron can cause symptoms less severe (Callaway and Ledford, 2021) (Kupferschmidt and Vogel, 2021) (Ren, Wang et al., 2022). Even so, the high transmission rate of Omicron will pose a significant challenge for diagnostics and vaccine strategies. Therefore, tracking the genetic shifts of these variants is significant. For these reasons, the genetic diversity of the S gene of Omicron variants isolated in Vietnam was investigated. By constructing a network, the genetic relationship of Omicron variants would be revealed, supporting the tracing of a infection source of a new outbreak in the future.

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Article source : Genetic diversity of SARS-CoV-2 Omicron variants’ spike gene in Vietnam   

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Molecular characterization of rice (Oryza sativa L.) genotypes using target region amplification polymorphism (TRAP) markers in relation to grain iron content

• Pavan J. Kundur1,2,3*, Prakash G. Patil1,4, B.G. Harish2, 3, C.K. Ramesh5, H.E. Shahidhar1

1. Department of Plant Biotechnology, University of Agricultural Sciences, Bengaluru -560065, India
2. M. S Ramaiah Institute of Technology, Bengaluru- 560054, India
3. Visveshwarya Technological University, Belagavi- 590018, India
4. Indian Institute of Pulses Research, Kanpur-208024, India
5. Sahyadri Science College, Shivamogga – 577203, India

In the present investigation, based on the seven rice putative candidate iron transporter genes, novel TRAP markers were developed.These markers were successfully employed in the molecular diversity study among 30 rice genotypes representing improved rice cultivars and land races with varied grain iron content (7.38 - 30.58 ppm).

Totally, thirty TRAP primer combinations were screened, which generated 703 bands out of which 654 were polymorphic (93%) with an average of 21.8 bands per primer combination. The average polymorphic information content (PIC) values ranged from 0.09(Osysl4b+ME05) to 0.25 (Osnramp5c+ME05, Osnramp1b+ME02 and Osysl4a +ME02). Gene diversity (H ˆ) ranged from 0.10 (Osysl4b+ME05) to 0.31 (Osnramp1b + ME02 and Osysl4a +ME02). The Jaccard dissimilarity ranged from 0.15 to 0.52, explaining 37% of genetic variation (Table 4).

Grouping of genotypes based on UPGMA and principal coordinate analysis (PCoA) were found comparable and grouping of genotypes into a different cluster was found mainly on the basis of pedigree relationships. TRAP markers revealed well resolved relationships among rice genotypes. The information generated from this study will helps to select parental combinations for breeding high iron content rice varieties.

Journal Name: International Journal of Agronomy and Agricultural Research (IJAAR)

Publication Name: International Network For Natural Sciences (INNSPUB)

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