scholarly journals Evaluation of the genetic diversity of six Chinese indigenous chickens

2020 ◽  
Vol 33 (10) ◽  
pp. 1566-1572
Author(s):  
Yuzhu Sha ◽  
Caixia Gao ◽  
Meimei Liu ◽  
Shengguo Zhao
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Indian Subcontinent ◽  
Coastal Region ◽  
Principal Component ◽  
Sharp Decrease ◽  
Haplotype Sharing ◽  
Indigenous Chickens ◽  
D Loop ◽  
Commercial Chickens

Objective: The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China.Methods: In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds.Results: Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious.Conclusion: The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

scholarly journals Evolutionary processes involved in the emergence and expansion of an atypical O. sativa group in Madagascar.

2020 ◽  
Author(s):  
Nourollah Ahmadi ◽  
Alain Ramanantsoanirina ◽  
João D. Santos ◽  
Julien Frouin ◽  
Tendro Radanielina
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Indian Subcontinent ◽  
Principal Component ◽  
Feature Space ◽  
Whole Genome ◽  
Human Settlement ◽  
Evolutionary Processes ◽  
Assignment Method ◽  
Asian Rice

Abstract Understanding crops genetic diversity and the evolutionary processes that accompanied their world-wide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement was accompanied by the introduction of Oryza sativa. Early studies had reported the presence in the island of a rice group specific to Madagascar. Using 24K SNP, we compared diversity patterns at the whole genome and at haplotypes (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1,929 Asian rice accessions. The haplotypes level analysis aimed at identifying local genotypic variations, relative to the whole genome level, using a group assignment method that relies on kernel density estimation in a Principal Component Analysis feature space. Migration bottleneck had resulted in 10–25% reduction of diversity among the Malagasy representatives of indica (G1) and japonica (G6) populations. Compared to their Asian counterpart, G1 and G6 showed slightly lower indica and japonica introgressions, suggesting the latter population had undergone less recombinations when migration to the island occurred. The origins of G1 and G6 was delineated to XI-2 indica subpopulation from the Indian subcontinent and to tropical japonica from the Malay Archipelago, respectively. The Malagasy-specific group (Gm) had a rather high gene diversity and an original haplotype pattern: much lower share of indica haplotypes, and much higher share of Aus and japonica haplotypes than G1 and indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-cAus admixes and “Bulu” type landraces of G6 in the highlands of Madagascar, and to human selection for adaptation to the lowland ecosystems of the highlands. Pattern of rice genetic diversity was also tightly associated with the history of human settlement in the island. Emergence of the Gm group is associated with the latest arrivals of Austronesians, who founded the Merina kingdom in the central highlands and developed lowland rice cultivation. As an intermediary form between Aus, indica and japonica, the three pillars of O. sativa domestication, Gm represents a very valuable genetic resource in breeding for adaptation to cold tolerance in tropical highlands.

scholarly journals Evolutionary Processes Involved in the Emergence and Expansion of an Atypical O. sativa Group in Madagascar

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Nourollah Ahmadi ◽  
Alain Ramanantsoanirina ◽  
João D. Santos ◽  
Julien Frouin ◽  
Tendro Radanielina
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Indian Subcontinent ◽  
Principal Component ◽  
Feature Space ◽  
Rice Cultivation ◽  
Lowland Rice ◽  
Whole Genome ◽  
Human Settlement ◽  
Evolutionary Processes

AbstractUnderstanding crops genetic diversity and the evolutionary processes that accompanied their worldwide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement brought the introduction of Oryza sativa. Early studies in the island had reported the presence of a rice group specific to Madagascar. Using 24 K SNP, we compared diversity patterns at the whole genome and at haplotype (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1929 Asian rice accessions. The haplotype level analysis aimed at identifying local genotypic variations, relative to the whole genome level, using a group assignment method that relies on kernel density estimation in a Principal Component Analysis feature space. Migration bottleneck had resulted in 10–25% reduction of diversity among the Malagasy representatives of indica and japonica populations. Compared to their Asian counterpart, they showed slightly lower indica and japonica introgressions, suggesting the two populations had undergone less recombination when migration to the island occurred. The origins of the Malagasy indica and japonica groups were delineated to indica subpopulation from the Indian subcontinent and to tropical japonica from the Malay Archipelago, respectively. The Malagasy-specific group (Gm) had a rather high gene diversity and an original haplotype pattern: much lower share of indica haplotypes, and much higher share of Aus and japonica haplotypes than indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-Aus admixes and “Bulu” type landraces of japonica in the central high plateaux of Madagascar, and to human selection for adaptation to the lowland rice cultivation. Pattern of rice genetic diversity was also tightly associated with the history of human settlement in the island. Emergence of the Gm group is associated with the latest arrivals of Austronesians, who founded the Merina kingdom in the high plateaux and developed lowland rice cultivation. As an intermediary form between Aus, indica and japonica, the three pillars of O. sativa domestication, Gm represents a very valuable genetic resource in breeding for adaptation to cold tolerance in tropical highlands. We proposed the name Rojo for this new rice group.

scholarly journals A PRELIMINARY COMPARISON OF MITOCHONDRIAL D-LOOP REGION OF FUNAAB ALPHA AND NIGERIAN INDIGENOUS CHICKENS

2021 ◽  
Vol 20 (1) ◽  
pp. 1-11
Author(s):  
S.O. DUROSARO ◽  
B.T. OSHINOWO ◽  
A.C. AKPOJO ◽  
L.T. OLUYOMBO ◽  
I.C. NWOSU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Nucleotide Polymorphisms ◽  
Indigenous Chickens ◽  
Loop Region ◽  
D Loop ◽  
Selective Forces ◽  
Loss Of Diversity

Nigerian indigenous chickens possess immunity from endemic diseases and have a better survival rate than commercial hybrid strains under local production conditions. FUNAAB Alpha chicken was developed by improving Nigerian indigenous chickens through crossbreeding and selection. This study compared the mitochondrial d-loop of FUNAAB Alpha and Nigerian indigenous chickens to check likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Blood samples were collected from Nigerian indigenous (n=23) and FUNAAB Alpha (n=20) chickens sampled from farms and houses in Ogun state, Nigeria. The Hypervariable 1 (HV1) of the mitochondrial d-loop region was amplified and sequenced. Single nucleotide polymorphisms present in HV1 of chickens were identified using Clustal W. Genetic diversity of the region was determined using DnaSp v5 while selective forces acting on the chickens were predicted using HyPhy software implemented inside MEGA 6 software. Phylogenetic relationship among FUNAAB Alpha, Nigerian indigenous and other chicken breeds was determined using MEGA 6 software. Five polymorphisms were identified in FUNAAB Alpha chickens while twelve were identified in Nigerian indigenous chickens. All the polymorphisms identified in FUNAAB Alpha chickens were also observed in Nigerian indigenous chickens while seven polymorphisms were unique to Nigerian indigenous chickens. Higher diversity indices were observed in Nigerian indigenous chickens (number of haplotype: 4; haplotype diversity: 0.743±0.012; nucleotide diversity: 0.014±0.0013 and average number of nucleotide differences: 4.332) compared with FUNAAB Alpha chickens (number of haplotype: 2; haplotype diversity: 0.485±0.001; nucleotide diversity: 0.008±0.0001 and average number of nucleotide differences: 2.424). Positive selective forces were acting on FUNAAB Alpha chickens while negative selective forces were acting on Nigerian indigenous chickens. Phylogenetic analysis revealed that FUNAAB Alpha chickens clustered with Nigerian indigenous and South American chickens. It can be concluded that there was likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Breeding programmes aimed at improvement of genetic diversity and reduction of genetic erosion should be applied in subsequent improvement of FUNAAB Alpha chickens.

scholarly journals Genetic Diversity of South African Indigenous Goat Population from Four Provinces Using Genome-Wide SNP Data

2020 ◽  
Vol 12 (24) ◽  
pp. 10361
Author(s):  
Tlou Caswell Chokoe ◽  
Khanyisile Mdladla-Hadebe ◽  
Farai Muchadeyi ◽  
Edgar Dzomba ◽  
Tlou Matelele ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
South African ◽  
Principal Component ◽  
Chromosome 8 ◽  
Nucleotide Polymorphisms ◽  
North West ◽  
Genome Wide ◽  
Goat Population ◽  
Indigenous Goat

Genome-wide assessments of the genetic landscape of Farm Animal Genetic Resources (FAnGR) are key to developing sustainable breed improvements. Understanding the FAnGR adaptation to different environments and supporting their conservation programs from community initiative to national policymakers is very important. The objective of the study was to investigate the genetic diversity and population structure of communal indigenous goat populations from four provinces of South Africa. Communal indigenous goat populations from the Free State (FS) (n = 24), Gauteng (GP) (n = 28), Limpopo (LP) (n = 30), and North West (NW) (n = 35) provinces were genotyped using the Illumina Goats SNP50 BeadChip. An Illumina Goats SNP50 BeadChip data from commercial meat-type breeds: Boer (n = 33), Kalahari Red (n = 40), and Savanna (n = 31) was used in this study as reference populations. The Ho revealed that the genetic diversity of a population ranged between 0.39 ± 0.11 Ho in LP to 0.42 ± 0.09 Ho in NW. Analysis of molecular variance revealed variations of 3.39% (p < 0.0001) and 90.64% among and within populations, respectively. The first two Principal Component Analyses (PCAs) revealed a unique Limpopo population separated from GP, FS, and NW communal indigenous goat populations with high levels of admixture with commercial goat populations. There were unique populations of Kalahari and Savanna that were observed and admixed individuals. Marker FST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest FST value (FST = 0.72; chromosome 8) was located on the UHRF2 gene. Population differentiation tests (PCAdapt) revealed PC2 as optimal and five outlier SNPs were detected on chromosomes 10, 15, 20, and 21. The study revealed that the SNPs identified by the first two principal components show high FST values in LP communal goat populations and allowed us to identify candidate genes which can be used in the development of breed selection programs to improve this unique LP population and other communal goat population of FS, GP, and NW, and find genetic factors contributing to the adaptation to harsh environments. Effective management and utilization of South African communal indigenous goat populations is important, and effort should be made to maintain unique genetic resources for conservation.

scholarly journals Genetic polymorphisms on heat-shock protein 70 gene and mitochondrial DNA d-loop variations: implications on selection for heat stress in indigenous chickens in Kenya

2019 ◽  
Author(s):  
Grace M Kennedy ◽  
Philip M Panyako ◽  
Philip A Oyier ◽  
Emmanuel K Ndiema ◽  
Jacqueline K Lichoti ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Heat Stress ◽  
Heat Shock Protein 70 ◽  
Diversity Indices ◽  
Hsp70 Gene ◽  
Indigenous Chicken ◽  
Turkana Basin ◽  
Indigenous Chickens ◽  
D Loop ◽  
Commercial Chickens

Background: Climate change resulting in heat stress, is one of the most challenging environmental conditions affecting poultry. Studying thermotolerance is crucial in the prevention of heat stress in chickens because it may lead to the identification of genetic lines that can withstand adverse effects of heat stress. This study aimed at investigating polymorphisms in heat shock protein 70 (HSP70) gene in indigenous chicken ecotypes. We also analyzed the mitochondrial DNA (mtDNA) D-loop of indigenous chickens to assess their origins and genetic diversity. Methods: We collected samples From Turkana basin, Mt. Elgon catchment, Lake Victoria basin and Lamu chicken ecotypes in Kenya. Genomic DNA was extracted from 280 chicken samples. The first 360 bp region of HSP70 and the first 760 bp region of the mtDNA were then amplified via PCR. These were later sequenced using Sanger ABI 3730 method. Results: We reveal through a detailed analysis of the HSP70 gene fragment in 20 indigenous chickens the presence of three HSP70 haplotypes (GC, AC, and AG) and 28 mtDNA haplotypes. Phylogenetic analysis of HSP70 revealed the presence of the ancestral haplotype GC which dominated in Turkana basin ecotype. The 28 mtDNA haplotypes clustered in haplogroups A, B, C, D, E and I. Haplogroup E which has never been reported in commercial chickens dominated in Turkana basin ecotype indicating no admixture with commercial chickens. mtDNA haplogroups were shown to have originated from various parts of South and Southeast Asia. Lack of population structure in indigenous chicken ecotypes could be an indication of genetic admixture. The mtDNA nucleotide and haplotype diversity indices were low for Turkana basin ecotype and high for Lamu ecotype. High HSP70 nucleotide diversity indices were recorded in Turkana basin ecotype, while low values were recorded in Lamu ecotype. Most of the mtDNA genetic variations occurred within individuals for the three hierarchical categories considered while most variations in HSP70 gene occurred within populations. Conclusions: This is the first study to analyze the HSP70 polymorphisms in indigenous chickens in Africa and results obtained should pave the way for further in-depth studies on heat stress.

scholarly journals Genetic polymorphisms on heat-shock protein 70 gene and mitochondrial DNA d-loop variations: implications on selection for heat stress in indigenous chickens in Kenya

2019 ◽  
Author(s):  
Grace M Kennedy ◽  
Philip M Panyako ◽  
Philip A Oyier ◽  
Emmanuel K Ndiema ◽  
Jacqueline K Lichoti ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Heat Stress ◽  
Heat Shock Protein 70 ◽  
Diversity Indices ◽  
Hsp70 Gene ◽  
Indigenous Chicken ◽  
Turkana Basin ◽  
Indigenous Chickens ◽  
D Loop ◽  
Commercial Chickens

Background: Climate change resulting in heat stress, is one of the most challenging environmental conditions affecting poultry. Studying thermotolerance is crucial in the prevention of heat stress in chickens because it may lead to the identification of genetic lines that can withstand adverse effects of heat stress. This study aimed at investigating polymorphisms in heat shock protein 70 (HSP70) gene in indigenous chicken ecotypes. We also analyzed the mitochondrial DNA (mtDNA) D-loop of indigenous chickens to assess their origins and genetic diversity. Methods: We collected samples From Turkana basin, Mt. Elgon catchment, Lake Victoria basin and Lamu chicken ecotypes in Kenya. Genomic DNA was extracted from 280 chicken samples. The first 360 bp region of HSP70 and the first 760 bp region of the mtDNA were then amplified via PCR. These were later sequenced using Sanger ABI 3730 method. Results: We reveal through a detailed analysis of the HSP70 gene fragment in 20 indigenous chickens the presence of three HSP70 haplotypes (GC, AC, and AG) and 28 mtDNA haplotypes. Phylogenetic analysis of HSP70 revealed the presence of the ancestral haplotype GC which dominated in Turkana basin ecotype. The 28 mtDNA haplotypes clustered in haplogroups A, B, C, D, E and I. Haplogroup E which has never been reported in commercial chickens dominated in Turkana basin ecotype indicating no admixture with commercial chickens. mtDNA haplogroups were shown to have originated from various parts of South and Southeast Asia. Lack of population structure in indigenous chicken ecotypes could be an indication of genetic admixture. The mtDNA nucleotide and haplotype diversity indices were low for Turkana basin ecotype and high for Lamu ecotype. High HSP70 nucleotide diversity indices were recorded in Turkana basin ecotype, while low values were recorded in Lamu ecotype. Most of the mtDNA genetic variations occurred within individuals for the three hierarchical categories considered while most variations in HSP70 gene occurred within populations. Conclusions: This is the first study to analyze the HSP70 polymorphisms in indigenous chickens in Africa and results obtained should pave the way for further in-depth studies on heat stress.

Genetic resources of Asian palmyrah palm (Borassus flabellifer L.): a comprehensive review on diversity, characterization and utilization

2021 ◽  
pp. 1-9
Author(s):  
S. Siju ◽  
K. K. Sabu
Keyword(s):  
Genetic Diversity ◽  
Southeast Asia ◽  
Genetic Resources ◽  
Indian Subcontinent ◽  
Crop Improvement ◽  
Research Gaps ◽  
Effective Utilization ◽  
Male And Female ◽  
Comprehensive Review ◽  
Comprehensive Information

Abstract Asian palmyrah palm (Borassus flabellifer L.) is a multipurpose, economically important tree widely distributed in the Indian subcontinent and Southeast Asia. The multifaceted uses (~800 uses) of the tree as food, wood and medicine make it a viable industrial crop. However, the dioecious nature of the tree coupled with long juvenile phase (12–20 years to initiate flowering), long stature and considerable variations in the productivity of male and female trees necessitates the application of new biotechnological tools for crop improvement. This review provides comprehensive information on the extent of genetic diversity of the crop, problems associated with palmyrah cultivation along with its multifaceted application and research gaps to be addressed for the effective utilization and conservation of palmyrah palm genetic resources.

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