Genetic Distance Matrix Research Articles

Diversity of Improved Diploids and Commercial Triploids from Musa spp. via Molecular Markers

Banana breeding consists of obtaining diploid, triploid, and tetraploid intra- and interspecific hybrids by conventional breeding methods with the objective of aggregating characteristics of agronomic and commercial interest. Given the narrow genetic base of bananas, Embrapa’s Banana Genetic Breeding Program (BGBP) aims at crosses between improved diploids (ID) (ID × ID) and between improved diploids (ID) and commercial triploids (ID × CTP) and tetraploids (ID × CTT), in order to increase the genetic base and variability in bananas regarding agronomic traits of interest and resistance to main biotic and abiotic factors. These improved diploids are resistant to main fungal diseases such as yellow (YSD) and black Sigatoka (BSD) disease and Fusarium wilt (race 1 and subtropical race 4), the latter being one of the most devastating diseases in bananas. The genetic diversity between 22 improved diploids and seven commercial banana triploids was analyzed using DNA molecular markers. Five IRAP (Inter-Retrotransposon Amplified Polymorphism, 7 ISSR (Inter-Simple Sequence Repeats) and 12 SSR (Simple Sequence Repeat) markers were used. The genetic dissimilarity matrix was based on the Jaccard dissimilarity index; clusters were separated using the UPGMA (Unweighted Pair Group Method With Arithmetic Mean) method and cophenetic correlation of 0.8755. This study of the genetic diversity between improved diploids and commercial triploids, based on the genetic dissimilarity matrix, revealed that the most dissimilar diploids were DM23 and DM15 (74%) and DM16 and DM15 (74%). The smallest genetic distances between the improved diploids and commercial triploids were between TCGN25 and DM17 (50%) and TCN26 and DM17 (50%). The genetic distance matrix also revealed important genotypes to be used in crosses in order to maintain good characteristics in commercial triploids when crossed with improved diploids. The results of our study provide better breeding strategies for one of the largest banana-breeding programs worldwide focused on the development of banana varieties resistant to main biotic and abiotic factors.

Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip.

This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), polymorphic marker ratio (PN), expected heterozygosity (He), observed heterozygosity (Ho), effective number of alleles, and minor allele frequency (MAF). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient FROH was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (BMPR1B, KCNIP4, and FAM13A). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

Identification of DNA Barcodes from rbcL Chloroplast DNA in Katokkon Chili (Capsicum annuum var. chinense) Origin of Tana Toraja, South Sulawesi

Katokkon chili (Capsicum annuum var. chinense) is a type of chili which are commonly found in Tana Toraja. It has a distinctive aroma, high spiciness, and a potential economic value but has not been widely identified and explored, thus, it is necessary to carry out molecular identification using DNA barcodes from chloroplast DNA. The aim of this study was to determine genetic variation and the results of constructing a phylogenetic tree from DNA sequences katokkon chili (C. annuum var. chinense) using the rbcL marker. This study used 6 samples of katokkon chilies (C. annuum var. chinense) and 3 outgroup samples (C. frutescens, C. chinense and C. baccatum). The stages of the research included total DNA isolation, qualitative and quantitative tests, PCR amplification using rbcL primers, and sequencing. Data analysis used is sequence alignment, phylogenetic, genetic distance matrix, haplotypes and phylogeography. The results showed genetic variation with 7 polymorphisms consisting of 4 singleton sites at the nucleotide base sequences of 6th, 525, 715 and 737, and 3 parsimony informative sites at the nucleotide base sequences 370, 616 and 902 and the haplotype distribution is divided into 4 haplotypes namely Hap_1 (A1, A2, A3, B1, B2 and B3), Hap_2 (C1), Hap_3 (C2), and Hap_3 (C3). The phylogenetic tree construction formed two clades, namely clade I consist of six samples of katokkon chilies (C. annuum var. chinense) and clade II consisting of three outgroup samples. Mark the highest bootstrap is 96 and the lowest bootstrap value is 29. Genetic distance matrix values are in the range of 0.000–0.005.

Sequence Analysis of some species in the genus Amaranthus L. using Ribulose-1.5 - bisphosphate carboxylase/oxygenase (rbcL) genes

Bioinformatics is a novel method to investigate evolutionary relationships and genetic diversity among species. This study assessed the evolutionary patterns and genetic diversity of Amaranthus species using ribulose-1.5-bisphosphate carboxylase/oxygenase (rbcL gene). A total of 20 full FASTA-format rbcL gene sequences for accessions of Amaranthus tricolor, A. dubius, A. cruentus, A. viridis, and A. spinosus from different regions were retrieved from the National Center for Biotechnology Information. Multiple sequence alignment was used to determine genetic variations. A phylogenetic tree was constructed using neighbor-joining clustering method while a distant matrix was created using Tamura-Nei genetic distance model. From position 1 to 22 in nucleotide alignment, only accession KX082771.1 from USA, aligns. The exclusive alignment in this region suggests an exceptionally conserved sequence among species, implying a common genetic origin. However, from position 23 to 50, nine different accessions namely MN192576.1, MN204800.1, EF590496.1, GQ248546.1, OQ737000.1, MG246937.1, MN104855.1, MN104858.1, and MN04859.1 align. The phylogenetic tree representing the evolutionary relationships offers insights into the genetic diversity and relatedness of these species within specific regions. The genetic distance matrix shows that sequences within the same region share relatively high similarity scores, indicating a genetic connection likely influenced by their geographic proximity. However, sequences from different regions, exhibit moderate genetic differences, emphasizing the genetic diversity across geographically distinct regions. The observed genetic diversity and evolutionary relationships among accessions of Amaranthus revealed by rbcL genes highlight the unique genetic features of these species in different regions, and therefore should be explored for their genetic improvement and conservation purposes.

Contribution of environmental factors to genetic variation in the Pacific white-sided dolphin

Environmental changes driven by pollution and climate change have affected many species globally. The Pacific white-sided dolphin, or Lagenorhynchus obliquidens (L. obliquidens), is threatened by water pollution, which is the product of human actions and can impact the genetic structure of species in affected areas. While researchers have studied genetic differences between populations of L. obliquidens in Japan, they failed to explore the potential environmental drivers of these differences. Our research aimed to identify the major environmental factors impacting the genetic variation of L. obliquidens, which will increase our understanding of how this species responds to changes in the environment. We studied several different variables, including salinity, ocean currents, temperature, and microplastic levels. Due to the significant presence and variation of microplastics in the ocean surrounding Japan, we hypothesized that this would have the most notable impact on the genetic variation of L. obliquidens. We began our research by gathering genetic sequencing data from a preexisting study focusing on populations along the Japanese coast. We collected environmental data and analyzed it alongside a genetic distance matrix, leveraging data analysis and machine learning tools in R. We found that the most impactful variable was current stability, which did not match our original prediction of microplastic levels having the most significant impact. We then investigated why ocean currents may have had such a strong impact on L. obliquidens and proposed that it has a connection to nutrient and prey distribution, which can be majorly impacted by changes in ocean currents.

The impact of non-environmental factors on the chemical variation of Radix Scrophulariae

Radix Scrophulariae is a commonly used Chinese herb derived from the dried root of Scrophularia ningpoesis Hemsl. (S. ningpoensis). It is difficult to accurately estimate the dosage of Chinese medicinal materials used in the prescription because of the chemical variation caused by various factors. To analyze the non-environmental factors affecting the chemical variation of Radix Scrophulariae, we planted nine different cultivated varieties of S. ningpoensis in the same plantation. Based on sequence-related amplified polymorphism (SRAP), simple sequence repeats (SSR) markers and high-performance liquid chromatography (HPLC) analysis, we found that the materials from the cultivated varieties could be divided into two groups, the Zhejiang group, and the southwest China group. The genetic distance based on molecular data between the two groups was above 0.3882, and the Euclidean distance based on chemical data between the two groups was above 5.312. The correlation analysis between the genetic distance matrix based on SRAP and the Euclidean distance matrix based on 18 HPLC peaks of the whole underground part revealed that the genetic differentiation and chemical variation were positively related, r = 0.7196 (p < 0.05). The genetic background, different part of the roots and the different development of the roots are the three non-environmental factors causing the chemical variation. The coefficient of variation (C.V) of chemical composition of Radix Scrophulariae with different genetic background reached to 93.62 %, the C.V of the chemical composition of Radix Scrophulariae derived from the same variety reached to 64.21 %, the C.V of the chemical composition of Radix Scrophulariae derived from the middle part of the roots of S. ningpoensis from the same variety reached to 45.55 %. The C.V of chemical composition of Radix Scrophulairae produced in the same plantation could be controlled to 38.43 % by using the same variety of roots with the approximate mass derived from the middle part of the roots under 20 g. Our findings provided insights to decrease the chemical variation of Chinese medicinal materials by controlling non-environmental factors.

Conservation genetics of the protected candy barrel cactus Echinocactus platyacanthus in the Chihuahuan Desert Region

Three main genetic diversity hotspots were identified in a survey of the genetic variability of the populations of the candy barrel cactus Echinocactus platyacanthus, a protected and highly sought-after cacti for ornamental, culinary and livestock water source in the Chihuahuan Desert Region, Mexico. This study identified one southern, one central, and one northern population in the Chihuahuan Desert Region as first priorities for conservation based on the analysis of a matrix of 4 ISSRs for 183 individuals from 10 localities along the 900 × 300 air km polygon of the geographic distribution of the species. The genetic structure of the 183 individuals from the 10 populations studied, showed a high degree of genetic differentiation for each of the localities with low gene flow, making each of these populations important for conservation actions. The isolation by distance analysis showed that other factors apart from the geographic distance could be playing an important role in the differentiation of the genetic structure of the populations. The UPGMA tree derived from the genetic distance matrix showed that the central and the southern populations conform a mega genetic population clearly separated from the northern populations, each with its own genetic signature.

Anthropogenic and natural fragmentations shape the spatial distribution and genetic diversity of roe deer in the marginal area of its geographic range

Habitat destruction and fragmentation are major factors in the destruction of genetic diversity and affect the movement behavior of the Roe deer population in the remaining habitats. Here, we study the population and landscape genetics of Capreolus capreolus (roe deer) in northern and northwestern Iran using twelve polymorphism microsatellite markers. From 111 total specimens, 63 had successful extraction (6 feces, 35 tissues, 9 bones, and 13 antlers). We considered 30 microsatellite polymorphic loci, of which only 12 were amplified for our further analysis. For genetic diversity analysis, the Weir-Cockerham method was applied to measure the inbreeding coefficient (FIS) and fixation index (FST) for each locus as well as for each population. For landscape genetics, the susceptibility patterns of genetic variations were assessed using three hypotheses including isolation by distance (IBD), isolation by environment (IBE), isolation by resistance (IBR), and individual landscape genetic analysis. A habitat suitability map as an indicator of landscape resistance was constructed from several species distribution models (SDMs) algorithms including Generalized Boosting Models (GBM), Maximum Entropy (Maxent), Random Forest (RF), Generalized Linear Model (GLM), Multivariate Adaptive Regression Splines (MARS) and artificial neural networks (ANN) and an ensemble model. Our estimated FIs index showed that the Golestan, Arasbaran, and Guilan populations had the highest and lowest genetic diversity among roe deer populations. According to the Fst criterion, our results showed that Golestan and East Azarbaijan (Arasbaran) had the highest and Mazandaran had the lowest genetic distance patterns. Our results do not suggest that there is high genetic differentiation for roe deer in the region, with high levels of gene flow between study areas. We found that geographic distance has no significant relationship with genetic distance and that there is no significant relationship between the ecological niche non-similarity matrix and the genetic distance matrix. The most influential factors affecting gene flow in roe deer were aspect and elevation variables. The analysis suggests that the landscape has no significant influence on the structuring of the studied population and shows little genetic differentiation.

Analysis of genetic diversity and population structure in Cambodian melon landraces using molecular markers

Genetic diversity of Cambodian melons was evaluated by the analysis of 12 random amplified polymorphic DNA (RAPD) and 7 simple sequence repeat (SSR) markers using 62 accessions of melon landraces and compared with 231 accessions from other areas for genetic characterization of Cambodian melons. Among 62 accessions, 56 accessions were morphologically classified as small-seed type with seed lengths shorter than 9 mm, as in the horticultural groups Conomon and Makuwa. Gene diversity of Cambodian melons was 0.228, which was equivalent to those of the groups Conomon and Makuwa and smaller than those of Vietnamese and Central Asian landraces. A phylogenetic tree constructed from a genetic distance matrix classified 293 accessions into three major clusters. Small-seed type accessions from East and Southeast Asia formed clusters I and II, which were distantly related with cluster III consisting of large-seed type melon from other areas. All Cambodian melons belonged to cluster I (except three accessions) along with those from Thailand, Myanmar, Yunnan (China), and Vietnam (“Dua thom” in the northwest), thus indicating genetic similarity in these areas. In addition, the Cambodian melons were not differentiated among geographical populations. Conomon and Makuwa were classified into cluster II, together with melon groups from the plains of Vietnam. The presence of two groups of melons in Southeast Asia was also indicated by population structure and principal coordinate analysis. These results indicated a close genetic relationship between Cambodia and the neighboring countries, thus suggesting that Cambodian melons are not directly related to the establishment of Conomon and Makuwa.

Replicative Study in Performance-Related Genes of Brazilian Elite Soccer Players Highlights Genetic Differences from African Ancestry and Similarities between Professional and U20 Youth Athletes.

Classically, genetic association studies have attempted to assess genetic polymorphisms related to human physiology and physical performance. However, the heterogeneity of some findings drives the research to replicate, validate, and confirmation as essential aspects for ensuring their applicability in sports sciences. Genetic distance matrix and molecular variance analyses may offer an alternative approach to comparing athletes' genomes with those from public databases. Thus, we performed a complete sequencing of 44 genomes from male Brazilian first-division soccer players under 20 years of age (U20_BFDSC). The performance-related SNP genotypes were obtained from players and from the "1000 Genomes" database (European, African, American, East Asian, and South Asian). Surprisingly, U20_BFDSC performance-related genotypes had significantly larger FST levels (p < 0.00001) than African populations, although studies using ancestry markers have shown an important similarity between Brazilian and African populations (12-24%). U20_BFDSC were genetically similar to professional athletes, showing the intense genetic selection pressure likely to occur before this maturation stage. Our study highlighted that performance-related genes might undergo selective pressure due to physical performance and environmental, cognitive, and sociocultural factors. This replicative study suggests that molecular variance and Wright's statistics can yield novel conclusions in exercise science.

De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity in Maruca vitrata (F.), a Legume Pod Borer.

Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect's public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes. We discovered that trinucleotide repeats were the most predominant microsatellite motifs (61.53%), followed by dinucleotide repeats (23.50%) and tetranucleotide repeats (14.95%). Based on the analysis, twenty-five markers were selected for validation in M. vitrata populations collected from various regions of India. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) ranged from 2 to 5; 0.00 to 0.80; and 0.10 to 0.69, respectively. The polymorphic loci showed polymorphism information content (PIC), ranging from 0.09 to 0.72. Based on the genetic distance matrix, the unrooted neighbor-joining dendrogram differentiated the selected populations into two discrete groups. The SSR markers developed and validated in this study will be helpful in population-level investigations of M. vitrata to understand the gene flow, demography, dispersal patterns, biotype differentiation, and host dynamics.

Phylogeographic analysis of the Japanese wild boar (&lt;I&gt;Sus scrofa leucomystax&lt;/I&gt;)

The Japanese wild boar (Sus scrofa leucomystax) is an indigenous subspecies of the wild boar, which is distributed in Honshu, Shikoku, Kyushu, and other smaller islands of Japan. The distribution area of the Japanese wild boar has in the last 40 years expanded by 1.9-fold due to improved suitable survival conditions, such as global warming which has decreased snowfall, increased abandoned farmland, and decreased hunting pressure. As a result, the negative impacts of this population increase on humans continue to spread. In this study, 1,251 Japanese wild boars were sampled from 32 prefectures which nearly cover the entire expanded distribution area in Japan, and phylogeographical analysis was performed using 30 Measurement of Domestic Animal Diversity recommended microsatellite markers. Both neighbor-joining (NJ) phylogenetic trees constructed using Nei's DA genetic distance matrix and population genetic structure analysis classified Japanese wild boar into six phylogeographical subpopulations, including northern Honshu, eastern Honshu, central Honshu, western Honshu, Shikoku, and Kyushu. The six identified genetic subpopulations were speculated to form as a result of several factors, including human activity between the northern and eastern Honshu, occurrence of three mountain ranges of 3,000-meter height between the eastern and central Honshu, the inland sea between western Honshu and Shikoku, and the presence of strait between western Honshu and Kyushu. Interestingly, some individual wild boars from Gunma, Tochigi, and Miyazaki areas formed distinct and separate subpopulations, with animals within these subgroups exhibiting traits such as low genetic differentiation and high diversity, which likely suggested gene influx from domestic pigs or other sources.

Insights into the genetic landscape and presence of Cochliomyia hominivorax in the Caribbean.

The New World screwworm, Cochliomyia hominivorax, is a major parasite that causes myiasis in livestock, humans, and other warm-blooded animals in the western hemisphere. There is a permanent biological border that is maintained between Panama and Colombia, as it has been eradicated from North and Central America. However, it still exists in much of the Caribbean and South America causing an estimated annual loss of $3.6 billion dollars in South America alone. Less information is available for C. hominivorax in the Caribbean. Thus, here we examined its presence and genetic landscape in order to gain insights into this fly's distribution in this region. First, through sampling efforts, novel GPS (Global Positioning System) coordinates were collected. Second, the environmental correlates of those presence points were examined. Next, samples were sequenced in order to obtain a pairwise ΦIT genetic distance matrix. And lastly, this matrix was used to create a genetic landscape of divergence. The results of the genetic landscape show flies as more diverse in Trinidad and Tobago and less diverse in the Dominican Republic. This is perhaps due to the proximity of Trinidad to Venezuela and gene flow may be occurring between these two areas. This information will aid in screwworm surveillance and control programs by providing environmental correlates and a view into the distribution of these flies.

The morphological and molecular variability of Sporisorium scitamineum isolates from Eswatini

Sugarcane smut is a disease of economic importance in the sugarcane industry, occasioning losses of up to 50%. Current management practices have been ineffective in controlling the fungal disease, and hence the understanding of the pathogen and the development of appropriate control measures are required. This study investigates the morphology, virulence and molecular variability of Sporisorium scitamineum isolates from Eswatini to understand its pathogenicity for effective control. Fungal isolates were collected along the Sugarbelt in the Lowveld of Eswatini. The isolates were verified by polymerase chain reaction using the bE4 and bE8 specific primers with amplification of a 459bp fragment. The identity was further verified by DNA sequencing. The teliospores from the isolates were uniform in brown colour, spiny texture and circular shape. The teliospore sizes were significantly (P=0.05) different among the isolates. The isolate from Big-Bend had a mean spore diameter of 5.55µm, while Simunye, Nsoko and Mhlume had average diameters of 4.69µm, 4.98µm and 4.87µm, respectively. The documentation of the developmental stages revealed that the samples were of variable virulence with significantly (P=0.05) different rates of promycelium development. The variable virulence of the isolates was further confirmed by the in-vivo pathogen biomass quantification by RT-qPCR. Genetic distance matrix analysis and cluster analysis showed high homology (99-100%) among the local isolates which indicate that there is a low variability among the strains that are found in the selected sugarcane growing areas of Eswatini

Zavot cattle genetic characterization using microsatellites.

This study aimed to reveal the genetic diversity and phylogenetic relationship between intra- and inter-breeds of Zavot cattle raised locally in and around Kars province, Türkiye. A total of 209 [Zavot (ZAV) n = 49, Eastern Anatolian Red (EAR) n = 40, Simmental (SIM) n = 40, Brown-Swiss (BS) n = 40, and Holstein (HOLS) n = 40] non-related cattle without any clinical health problems were evaluated. Using the standard phenol-chloroform method, deoxyribonucleic acid (DNA) was isolated from blood samples and amplified by multiplex polymerase chain reaction (PCR) using 19 bovine-specific microsatellite markers. A capillary electrophoresis process was applied to the denatured PCR products. A total of 274 different alleles were identified, with an average of 10.29 and an average of effective alleles of 5.38. According to the genetic distance matrix between populations, the largest genetic distance was found between ZAV-HOLS (0.358) populations, while ZAV-EAR populations were located at the same roots. The largest FST value (0.072) was found among ZAV-HOLS populations. According to the factorial correspondence analysis (FCA) graph, each population was located separately but also showed a mixture, especially the ZAV, EAR, and BS populations. The average polymorphism information content (PIC) values were the lowest (0.44) for the BM2113 marker and the highest (0.92) for the TGLA53 marker. In conclusion, ZAV cattle bred in the Kars region were found to be completely separate from the BS and SIM breeds which were claimed to have contributed to the formation of the ZAV breed. Since currently the native breeds, which are symbolic of the region, inbreeding cannot be prevented, an increase in studies devoted to the protection of these breeds and the establishment of pure herds will be useful for the future of native cattle in Türkiye.

A deep learning approach to real-time HIV outbreak detection using genetic data.

Pathogen genomic sequence data are increasingly made available for epidemiological monitoring. A main interest is to identify and assess the potential of infectious disease outbreaks. While popular methods to analyze sequence data often involve phylogenetic tree inference, they are vulnerable to errors from recombination and impose a high computational cost, making it difficult to obtain real-time results when the number of sequences is in or above the thousands.Here, we propose an alternative strategy to outbreak detection using genomic data based on deep learning methods developed for image classification. The key idea is to use a pairwise genetic distance matrix calculated from viral sequences as an image, and develop convolutional neutral network (CNN) models to classify areas of the images that show signatures of active outbreak, leading to identification of subsets of sequences taken from an active outbreak. We showed that our method is efficient in finding HIV-1 outbreaks with R0 ≥ 2.5, and overall a specificity exceeding 98% and sensitivity better than 92%. We validated our approach using data from HIV-1 CRF01 in Europe, containing both endemic sequences and a well-known dual outbreak in intravenous drug users. Our model accurately identified known outbreak sequences in the background of slower spreading HIV. Importantly, we detected both outbreaks early on, before they were over, implying that had this method been applied in real-time as data became available, one would have been able to intervene and possibly prevent the extent of these outbreaks. This approach is scalable to processing hundreds of thousands of sequences, making it useful for current and future real-time epidemiological investigations, including public health monitoring using large databases and especially for rapid outbreak identification.

Determining the Genetic Difference of Some World Cotton Genotypes Using iPbs (Inter-Primer Binding Sequences) Retrotransposon Markers

ABSTRACT This research was carried out with the aim of revealing the genetic differences of 30 cotton varieties from 14 countries using the iPBS-retrotransposon marker method. Genetic differences were determined by using iPBS marker method in PCR for 30 cotton varieties. According to the genetic distance matrix obtained in the NTSYS-pc 2.10e program, the closest genotypes were determined to be AzGR-11468 (Azerbaijan) and Maydos Yerlisi (India), and the similarity value between them was found to be 0.0318. The most distant genotypes were determined to be Hill Cotton 3 (Bangladesh) and Shazbaz (Pakistan), and the similarity value between them was found to be 0.7572. When the dendrogram generated based on the UPGMA method was examined.30 cotton varieties were divided into 2 clades. According to the PCA made in the JMP program, the graphic results and eigen values obtained on the two-dimensional plane also supported these results. The first 3 eigen values explained 85% of the total variance in the population. Overall results suggest that Hill Cotton 3 (Bangladesh) (Gossypium arboreum) and Shazbaz (Pakistan) (Gossypium hirsutum) cultivars, which are the most distant relatives among 30 cotton genotypes, can be used as breeding cultivars in future cotton breeding studies.

Genetic diversity and population structure of 93 rice cultivars (lines) (Oryza sativa Xian group) in Qinba in China by 3 types of genetic markers

BackgroundThe Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice.MethodsFifteen phenotypic traits, a core set of 48 SSR markers which originated protocol for identification of rice varieties-SSR marker method in agricultural industry standard of the People's Republic of China (Ministry of Agriculture of the PRC, NY/T1433-2014, Protocol for identification of rice varieties-SSR marker method, 2014), and SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples.ResultsThe average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs.ConclusionsThe population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.

Evolutionary patterns of plastome resolve multiple origins of the Ns-containing polyploid species in Triticeae

Tracing evolutionary history proves challenging for polyploid groups that have evolved rapidly, especially if an ancestor of a polyploid is extinct. The Ns-containing polyploids are recognized as the NsXm and StHNsXm genomic constitutions in Triticeae. The Ns originated from Psathyrostachys, while the Xm represented a genome of unknown origin. Here, we use genetic information in plastome to trace the complex lineage history of the Ns-containing polyploid species by sampling 26 polyploids and 90 diploid taxa representing 23 basic genomes in Triticeae. Phylogenetic reconstruction, cluster plot of genetic distance matrix, and migration event demonstrated that (1) the Ns plastome originated from different Psathyrostachys species, and the Xm plastome may originate from an ancestral lineage of Henrardia, Agropyron, and Eremopyrum; (2) the Ns, Xm, and St genome donors separately served as the maternal parents during the speciation of the Ns-containing polyploid species, resulting in a maternal haplotype polymorphism; (3) North AmericanLeymusspecies might originate from colonization during late Miocene via the Bering land bridge and were the paternal donor of the StHNsXm genome Pascopyrum species. Our results shed new light on our understanding of the rich diversity and ecological adaptation of the Ns-containing polyploid species.

Resistance to multiple leaf diseases in popcorn lines with potential for baby corn production

The cultivation of special corns, such as baby corn, has had a positive influence on the economy of the country. Despite its importance, there is still a need for studies aimed at increasing production and planting areas of the crop. Phytosanitary studies are of particular interest, as the cultivation of such crops is susceptible to a series of pathogens, such as Bipolaris maydis, Exserohilum turcicum, and Puccinia polysora. The use of resistant cultivars is the most effective way to prevent the occurrence of these diseases. Thus, the present study aimed to identify popcorn lines that have the potential for baby corn production and are resistant to the main leaf diseases that affect the crop. The experiment was conducted in randomized blocks with four replications of 30 lines in each area, during two planting seasons. The area was located at the Federal Institute of Espírito Santo (IFES) Campus of Alegre, situated in Rive district, Espírito Santo State, Brazil. Using the obtained data, the area under the disease progress curve was obtained. Subsequently, analysis of the joint variance of the data was conducted, and when a significant effect was found, a grouping of means test was conducted. The Mahalanobis distance for each pair of lines was also calculated, and the genetic distance matrix was used to construct a dendrogram using the UPGMA method. Considering the averages obtained for the three diseases (Southern corn leaf blight, Northern corn leaf blight, and Southern rust), lines L61, L63, L65, L683, L684, L685, L691, L694, and L695 were identified as possible donors of resistance alleles for multiple diseases. Multivariate analysis efficiently grouped the lines L61, L63, L684, L685, and L691, which are described as most resistant in the univariate analysis.