Publication quantitative
According to the data presented in the statistical graph of the research area, the scientific production of ROH and its genetic diversity vary over time. It began with modest production in 2009, followed by a slight increase in 2015, and as of 2017, there has been considerable growth in relevant studies in this field. It is important to note that the first approaches to genomic technologies applied to ROHs were recent, as demonstrated by the number of articles published in the first few years, as shown in Fig. 1.
The increase in the number of publications from 2017 onward was probably due to the implementation and maturity of nucleic acid sequencing, as well as the high availability of information in public and private databases. Finally, between 2014 and 2022, the number of publications increased annually. Thus, as shown in Fig. 1, studies of ROH and gene diversity have focused more on the field of molecular genetics in recent years. The main information collected for a review of the literature on runs of homozygosity (ROH) and genomic diversity is shown in Table 1. The results show that interest in this field is increasing, with an annual growth rate of 12.69%. The findings showed that ROH and genetic diversity are active and relevant fields, with each article receiving an average of 17.08 citations, demonstrating that ROH is important to the scientific community.
Table 1 Main information on the survey carried out.
Description
|
Results
|
Timespan
|
2009:2023
|
Sources (journals)
|
87.00
|
Documents
|
406.00
|
Annual growth rate %
|
12.69
|
Document average age
|
3.62
|
Average citations per doc
|
17.08
|
References
|
13.55
|
Autor’s keywords (de)
|
834.00
|
Authors
|
2317.00
|
Authors of single-authored docs
|
1.00
|
Coauthors per doc
|
7.64
|
International coauthorships %
|
51.23
|
Most relevant journals associated with genomic diversity and ROH
All the relevant literature related to these fields of genetics was published in 87 sources or journals, 7 of which published more than 15 documents (Fig. 2). In this respect, an analysis of the published documents reveals a significant interest in genetic diversity and ROH, as reflected in the approach of the journals.
International Collaboration
In recent years, research into gene diversity and ROH has attracted interest among scientists worldwide. A bibliometric analysis revealed that researchers from 95 countries had significant academic output in the area, totaling 406 relevant publications in the period 2009-2023. Asian, American, and European research institutes have proven to be the main drivers of this scientific production. These studies show a global and multidisciplinary interest in this complex subject. In brief, ROH is a globally relevant and active area of study, with researchers from many different countries taking part. Table 2 provides an overview of the corresponding authors' countries.
From the perspective of interconnectivity or networking the Single Country Publication (SCP), measures the level of intra-country collaboration; and the Cross-Country Collaboration Index (MCP), on the other hand, aims to monitor scientific collaboration between authors from different countries (Table 2).
China's intra-country cooperation (SCP) is significantly more important than its intercountry cooperation (MCP). This phenomenon can be due to the scale and diversity of the sinology. In contrast, the U.S. is the third largest academic power, with 38 articles. However, it is worth noting that the proportion of interaction documents is greater in international searches.
Table 2 The 10 most prolific countries in genetic diversity and ROH, corresponding author’s affiliation considered.
Country
|
N° of Articles
|
Frequency of total
|
*SCP
|
*MCP
|
China
Italy
Estados Unidos
Spain
|
79
|
0.302
|
56
|
23
|
40
|
0.153
|
28
|
12
|
38
|
0.145
|
16
|
22
|
21
|
0.08
|
07
|
14
|
Alemanha
Brazil
|
19
|
0.073
|
10
|
09
|
14
|
0.053
|
08
|
06
|
Canada
Iran
|
14
|
0.053
|
08
|
06
|
14
|
0.053
|
03
|
11
|
Netherlands
|
13
|
0.050
|
03
|
10
|
France
|
10
|
0.038
|
04
|
06
|
Total
|
262
|
1,000
|
143
|
119
|
*SCP= single country publications; *MCP= multiple country publications.
|
Table 3 presents the affiliations by field of study. The University of Palermo (Italy), Wageningen University and Research (Netherlands), and the Institute of Animal Science (China) emerge as leaders with 36, 33, and 32 publications, respectively.
The University of Edinburgh (United Kingdom) and Copenhagen University (Sino-Denmark) also make significant contributions, with 26 and 21 articles, respectively. The range of contributors continues remarkably, with associations from many countries, including United States, Spain and Brazil.
Table 3 Top 10 affiliations in the publications involving genetic diversity and ROH.
Affiliations
|
Number of articles
|
Articles (%)
|
Country
|
Univ Palermo
|
36
|
0,149
|
Italy
|
Wageningen Univ and Res
|
33
|
0,137
|
Nettherlands
|
Inst Anim Sci
|
32
|
0,133
|
China
|
University Edinburgh
|
26
|
0,108
|
USA
|
University Copenhagen
|
21
|
0,087
|
China
|
Cornel University
|
19
|
0,079
|
United State
|
Univ Calif Los Angeles
|
19
|
0,079
|
United State
|
Univ Zagreb
|
19
|
0,079
|
Croatia
|
China Agricultural University
|
18
|
0,075
|
China
|
Swedish Univ Agr Sci
|
18
|
0,075
|
Sweden
|
Total
|
241
|
1,00
|
|
Most relevant document
The 10 most cited articles had a total of 1,858 citations (Figure 3). These articles were distributed across 9 different scientific journals. The most cited article is the paper titled " Genomic Patterns of Homozygosity in Worldwide Human Populations", written [15] and published in The American Journal of Human Genetics (SJR factor 9,8), with a total of 314 citations.
Although the journal Nature Genetics is not the main resource, it is important to note that this article received a significant number of citations. Interestingly, the authors of the most cited articles include two (the authors) of the 10 most productive researchers.
Notably, eight of the ten most cited articles were published after 2013, confirming the results observed in annual scientific production (see Fig. 1). The growing trend of research into genetic polymorphisms and ROH, especially since 2017, demonstrates the heterogeneity of population genomics studies and the detection of genetic hybridization through ROH.
Researchers are exploring new approaches, such as how evolutionary factors, such as demography, assembly, and specific selection pressures, affect the population’s genomic structure. This study reports on a comprehensive population genome analysis.
Most frequent keywords
From a quantitative analysis, 3121 keywords were identified that were used repeatedly by the authors of the publications under analysis. These terms, endowed with specificity, effectively represent the content described in the texts. When evaluating the main meaning of these words, "homozygosity", "run" and "genetic diversity" were distinguished. These terms are emerging as central pillars of gene diversity and ROH research. These concepts have evolved remarkably over the years, revealing progressive interest and deepening (Fig. 4).
Over time, the information demonstrated a continuous and significant increase in keywords. Fig. 4. In 2023, as an example, the word "homozygosity" is recorded a significant total of 154 times, while "breed" reaches the mark of 143 occurrences.
In addition, the term "genetic diversity" appeared 95 times, showing a strong interest on ROH to elucidate biodiversity availability. The analysis also revealed that 'association' or ‘selection', has a relevant approach, with occurrences of 90, and 67 records, respectively. Also notable is the frequency of “linkage disequilibrium" term appears. In addition to the significant presence of goal of "conservation" (38), as well as the importance of "history" (50), which signals an increase in its occurrence over the years, see Fig.4.
Thematic map
The use of a thematic map becomes relevant when co-word analysis is used to trace the structure of a specific discipline. The main objective of this approach is to trace the conceptual structure using a term co-occurrence network to map and group keyword terms, subheadings, or abstracts in a bibliographic compilation [22, 25].
Data analysis under a quantitative approach revealed the emergence of four different thematic regions, where each region was in a specific quadrant (Fig. 5). In the upper right quadrant, specialization themes such as "homozygosity", "runs", "genetic diversity", "association" and "linkage" are highlighted.
These themes stand out due to their high density and outstanding centrality and play a fundamental role in structuring research fields, which has become a relevant component [9, 22].Conversely, the topics in the upper left quadrant preserve intrinsic links and correspond to areas of rapid development, which is reflected in their greater density, despite their more modest centrality. These topics, such as "r packhage", "demografic history", "hybridization" and "models", are specialized and peripheral (Fig. 4).
In the bottom left corner of the map, topics considered marginalized and underdeveloped can be examined; although these topics are sound to a certain extent, their centrality and decreasing density indicate incipient growth or even the possibility of expansion. There are links to topics such as "genomes" and "positive selection" (Fig. 5).
Finally, the topics in the lower right quadrant are substantial, wide-ranging, and cross-cutting, characterized by their high centrality. However, they have a relatively low density. Topics such as "homozygosity", "evolution", "inbreeding depression", "mutations", "sequence" and "alignment" in this quadrant signal convergence in the study of genetic diversity and ROH in many species, from humans to different pets. However, these topics are still under development and will form the basis and coverage for the near future.
Applied Methodologies
The functional analysis of runs of homozygosity (ROH) is supported by computational tools that play a key role in detecting and characterizing these genomic regions. Among the usual tools used to analyze SNP microarray data, PLINK software [26, 27] the most used program. A total of 37 articles published between 2013 and 2017 demonstrated the efficacy of utilizing PLINK software, with its superiority observed in 33 of these studies (Fig. 6).
However, relevant transformations have occurred in the software applications landscape. From 2018 to 2020, the PLINK software remained the most used, being cited in 60 studies. On the other hand, the rise of the R detectRUNS program was seen as a viable option, with its use in 12 studies during this period.
Between 2021 and 2023, there was a significant increase in the variety of software used. PLINK continued to be the most used, present in 86 searches, followed by detectRUNS v. 0.9.5, which appeared in 48 articles. Furthermore, other software programs were explored, highlighting the search for more comprehensive and accurate analytical methods during this period
Publications Analysis Based on Animal Diversity
The analysis of approximately 275 documents allows us to verify that ROH research requires a careful sampling methodology to assess the distribution of genotypes in animal populations, both domestic and wild. Based on the data provided, a sample covered a diverse set of species, including Human (25), cattle (68), sheep (54), pig (35), goat (23), chickens (25), other domestic and wild animals (59) (Fig. 7).