Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book:the case of the Pura Raza Española horse

Background:Estimating inbreeding,which is omnipresent and inevitable in livestock populations,is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding.Inbreeding coefficients have been historically estimated by using pedigree information;however,over the last decade,genome-base inbreeding coefficients have come to the forefront in this field.The Pura Raza Espanola(PRE)horse is an autochthonous Spanish horse breed which has been recognised since 1912.The total PRE population(344,718 horses)was used to estimate Classical(F),Ballou’s ancestral,Kalinowski’s ancestral,Kalinowski’s new and the ancestral history coefficient values.In addition,genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques(methods of moments-FHOM-,the diagonal elements of the genomic-FG-,and hybrid matrixes-FH-)and ROH measures(FRZ).The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse,with proven parenteral information for the last 40 years and a high degree of completeness(over 90%for the last 70 years)will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.Results:The mean values of the pedigree-based inbreeding coefficients ranged from 0.01(F for the last 3 generations-F3-)to 0.44(ancestral history coefficient)and the mean values of genomic-based inbreeding coefficients varied from 0.05(FRZ for three generations,FH and FHOM)to 0.11(FRZ for nine generations).Significant correlations were also found between pedigree and genomic inbreeding values,which ranged between 0.58(F3 with FHOM)and 0.79(F with FRZ).In addition,the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values,and the opposite when ancient values are calculated.Conclusions:Ultimately,our results show that it is still useful to work with a deep and reliable pedigree in pedigreebased genetic studies with very large effective population sizes.Obtaining a satisfactory parameter will always be desirable,but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

Seed Morphology and Seedling Variation of Four Ornamental Lupin Pedigrees

[Objective] This study was conducted to reveal seed characteristics, variation and their effects on seedling growth of ornamental lupins. [Method] The phenotypic characteristics and germination rate of the seeds of four excellent lupin pedigrees were measured, and then their correlations with seeding growth were analyzed. [Result] There were abundant variations among the four ornamental lupin pedigrees. Pink seeds had the largest volume and red seeds had the largest 1 000seed weight. The variation coefficients for the seed morphological traits among the four pedigrees ranged from 2.97% to 14.34%. Seed specific weight and 1 000-seed weight could be used as important indicators for selection in breeding because of their higher variability. Seed weight variation of ornamental lupin was mainly depen- dent on seed width variation. There was small variation in seed length. The seeds of the four ornamental lupin pedigrees started to germinate one day after sowing, and the germination period was 5 d. Germination rate coefficient and germination index of pink and red seeds were higher than those of blue seeds, but blue seeds had the largest germination rate. 1 000-seed weight shared significantly positive correlations with seed germination rate, germination potential and seedling retention rate. Round and large seeds had some advantages in germination. Full seeds had higher germination rate and speed, and seedling retention rate. There was a significant relationship between seed length-width ratio and the number of leaflets of seedlings. [Conclusion] The results provided references for the evaluation of seed phenotypic diversity and breeding research of ornamental lupins.

Pedigree and Trait Analysis of Soybean Varieties Registered in Henan Province

To elucidate the genetic relationship of the soybean varieties registered in Henan province, we analyzed the pedigrees, the major agronomic traits, and the eco- nomic traits of 74 soybean varieties registered in Henan province from 1985 to 2012, with reference to experience and technologies beneficial to breeding. The resuits indicated that these varieties originated from 113 parents, and positive correla- tion between the yield and the number of original parents was significant. In the major agronomic traits, the growth stage was about 106 days with relatively small variation, while the final height varied largely among these varieties. Among the fac- tore affecting the final yield, the pod number per plant exhibited an increasing trend, while the variation of 100-grain weight was relatively small. More than 50% of the 113 original parents came from Henan Province and its neighbor provinces, and the genetic relationship among the registered varieties was too close. The rational criteria of yield components of soybean varieties in Henan Province should be as fol- lows： the pod number per plant was about 48. 6, with 100-grain weight ranging from 17.55 g to 21.80 g.

Analysis of Pedigree and Trait Evolution of Peanut Varieties Registered in Fujian Province

In order to provide reference for the breeding of new peanut varieties and introduction of peanut cultivars in Fujian Province, the pedigree and trait evolution of 33 peanut varieties registered （certified, identified） during 1949-2011 in Fujian Province were analyzed. Results showed that, 45 parents were used as parents for peanut breeding, and 22 parents were originated from Fujian Province, 24 parents were registered varieties; Shitouqi, Yueyou 92, Shanyou 523, Quanhua No.10 and Quanhua 327 were milestone parents of peanut varieties in Fujian Province, and the phylogenetic relationship of varieties mainly came from Guangdong. Systematic se- lection was the main breeding method during 1951-1980 in Fujian Province, while crossbreeding became the main method of peanut breeding since 1991. With the variety update of peanuts, the yield levels were constantly increasing. The gradual increase of 100-pod weight and 100-kernel weight played an important role in the improvement of peanut yield. Fat content increased slightly with time, while protein content changed in contrast. Plant height was gradually decreased, and anti-lodging and fertilizer-tolerance capacity was improved, which were suitable for close planting. The total number of branches was decreased slightly, while the number of bearing branches barely changed.

Development of Genomic Microsatellite Multiplex PCR Using Dye-Labeled Universal Primer and Its Validation in Pedigree Analysis of Pacific Oyster(Crassostrea gigas)

There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.

OCCURRENCE CHARACTERISTIC OF KASHIN-BECK DISEASE BASED ON NUCLEAR FAMILY PEDIGREES

Objective The occurrence characteristic of Kashin Beck Disease (KBD) in pedigrees ascertained on the basis of one proband was estimated. Methods A total of 255 individuals in 40 pedigrees were collected from areas in the Shaanxi Province. Results ① Parents and siblings of index cases have a 3-4 times higher risk than a random unrelated individual. The odds ratio for disease is higher in mothers than in fathers of index cases; ② Prevalence in relatives of index cases (K r= 59.2% ) greatly exceeds population prevalence (K= 17.5% ); ③ K r increases with sibship size; ④ There is no significant difference of K r for male and female siblings of index cases. Also, population prevalence is not sex specific. Conclusion In conjunction with environmental agents, genetics may play an important role in KBD etiology.

Pedigree tracing of Fenneropenaeus chinensis by microsatellite DNA markers genotyping

Two microsateUite DNA loci were used to trace the pedigree structure of six families in the shrimp Fenneropenaeus chinensis. Four of the families were natural mating, and the others were mated by artificial insemination. Eleven alleles were acquired at two microsatellite DNA loci （locus RS0622 and locus EN0033 ） by investigating 145 offsprings and 11 parents. Five alleles were acquired from locus RS0622 and six from locus EN0033. As analyzed, the gene frequencies were between 0. 024 1 and 0. 493 1, the heterozygosity was 0.652 2 and 0.688 8, and the polymorphism information content （PIC） was 0.585 7 and 0.652 9 for the locus RS0622 and the locus EN0033, respectively. Twenty-three genotypes were detected and the genotypes of the losing parents were also inferred. The pedigrees of three F1 and three F2 generations were determined by matching the genotype at each locus.

Genetic relationship and pedigree of Chinese watermelon varieties based on diversity of perfect SNPs

Watermelon(Citrullus lanatus)is one of the world’s most important fruit crops,and China produces the most watermelons in the world.Recently,a watermelon variome consisting of 414 key resequenced accessions was reported.However,the genetic relationships and pedigree of Chinese watermelon varieties in the seed market remain unclear.In this study,241 evenly distributed perfect single nucleotide polymorphisms(SNPs)derived from the watermelon variome were selected for variety identification.The diversity of 247 Chinese watermelon varieties was identified based on their SNP genotypes.The 247 watermelon varieties were clustered into five subpopulations:the East Asian ecotype,intermediate ecotype,small fruit with red flesh ecotype,small fruit with yellow flesh ecotype,and American ecotype.We further established the pedigree of four subpopulations,of which JingXinNo.1,ZaoChunHongYu,HuangXiaoYu and XiaoLan,and Sugarlee were the main doner of the East Asian ecotype,small fruit with red flesh ecotype,small fruit with yellow flesh ecotype,and American ecotype,respectively.Thirty-two core SNPs were selected and applied in watermelon variety identification.They were also validated by the Kompetitive allele-specific PCR(KASPar)platform.The present study furthered our understanding of the genetic relationships and pedigree of watermelon varieties in China,and will help to manage the plant variety protection in watermelon.

POPULATION CHARACTERS IN HIGH RISK PEDIGREES OFNASOPHARYNGEAL CARCINOMA (NPC)

Objective: To investigate population characters in high risk pedigrees of NPC in Guangdong area and to explore the effect each other between tumor genetic susceptibility and infection of EB virus on pathogenic mechanism. Methods: Pedigree investigation, examination of DNA fingerprint, multi-antibodies of EB virus and nasopharyngeal cavity were done for all of the members in each high risk pedigree. Results: High positive rate of EBV VCA/IgA (23.22%), high percentage of high risk population of NPC (6.53–10.40%), high detected rate of malignant tumor (9552.59/105), and high detected rate of NPC (8464.32/105) were discovered and NPC was most common in first degree relative of a pedigree. Conclusion: Tumor genetic susceptibility, infection of EB virus might play a role in coordination of reinforced effect on occurrence of NPC.

Studies of a pedigree with limbal dermoid cyst

AIM: To study clinical features and gene mutations within the paired-like homeodomain transcription factor 2 (PITX2) gene in a pedigree of bilateral limbal dermoids. METHODS: Complete eye examinations have been performed on each individual of the family. Exons of paired-like homeodomain transcription factor 2 ( PITX2)were amplified by polymerase chain reaction, sequenced, and compared with a reference database. RESULTS: We described the phenotype, clinic findings in a family with two affected members. The masses of the proband's eyes were excised surgically demonstrating a dermoid cyst by histopathological examination. No mutation was detected in the gene PITX2 in this pedigree. CONCLUSION: A family of limbal dermoid cyst was reported. In addition, no pathogenic sequence variations were found in PITX2, indicating that this phenotype in this family is a distinctive entity.

SURGICAL MANAGEMENT OF EHLERS-DANLOS SYNDROME:FIRST REPORT OF A PEDIGREE IN CHINA

OBJECTIVE: To describe a case of Ehlers-Danlos syndrome type IV and its pedigree in China. METHODS: Clinical materials of a case of Ehlers-Danlos syndrome type IV and a pedigree of 6 members within 4 generations were analyzed. Dilated internal jugular vein in the proband was removed by operation. The diagnosis, surgical treatment, and postoperative complications were retrospectively reviewed. RESULTS: Vessels of the proband in the pedigree were crisp and easily lacinated during the procedure of removing his internal jugular vein. Repeating postoperative hematomas were found though complete stanching was achieved during the operation. The patient was successfully recovered by promptly debridgement and needle sucking. The other 5 members of the pedigree all had the triads of Ehlers-Danlos syndrome. CONCLUSIONS: Though it was of extremely low morbidity rate, the high mortality rate and complication of Ehlers-Danlos syndrome deserve great attention during surgical management, especially in patients with Ehlers-Danlos syndrome type IV. Surgeons should be aware of the ponderance of its complications and combined diseases to avoid fatal intraoperative vascular lascination and incontrollable hemorrhage.

Analysis on Some Agronomic Characters and Pedigree in Hezihao Series Peanut Varieties

The genealogical relationship and agronomic characters of 13 peanut varieties,breeded by Hezhou Academy of Agricultural Sciences,which had been authorized were analyzed.The results showed that 20 direct parents were involved in 13 varieties,80%of which came from Guangxi and Guangdong Province.Shanyou 523 and Yueyou 193 were used for more times;The genealogical analysis of these certified varieties can be traced back to 30 ancestral parents,the proportion of which contained consanguinity of Fu Peanut and Shitouqi were 84.62%.This demonstrated that genetic basis was rather narrow and it was quite difficult to make a great breakthrough in breeding.Plant height,total number of branches and oil content changed very little,100-pod weight and pod yield increased,whereas there was a downward trend in shelling percentage.Therefore,it is quite necessary to further broaden the germplasm basis of parents,enrich breeding methods,and continue to strengthen disease-resistant breeding and specific peanut breeding.

Pedigree and SSR Data Analysis Reveal Dominant Prevalence of Few Parents in Pedigrees of Pakistani Wheat Varieties

The international recognition of the importance of genetic diversity demands continuous estimation of genetic diversity of in hand population as test of its buffering capacity against all putative threats. Randomly selected Pakistani wheat varieties developed during 1965-1999 and 2000-2011 were evaluated on the basis of pedigree and SSR data. At 2nd and 3rd levels of pedigree, average occurrence of a parent per variety was 2.1 times. The dominating parents included BLUEBIRD, KALYANSONA and SIETE-CERROS-66, which were present in the pedigrees of 71.42%, 64.28%, and 58.57% varieties, respectively. The varieties INQLAB-91 and KIRAN-95 had the same pedigree and were genetically identical as revealed by SSR data. Similarly, varieties PAVON-76 and SOGHAT-90 also had the same parents in their pedigrees. This genetic similarity was also confirmed by SSR based cluster. The SSR based PC1 and PC2 showed narrow genetic diversity confirming the presence of few dominating parents. The results emphasize the inclusion of novel and genetically diverse parents in Pakistani wheat breeding programs to maintain broader genetic base of varieties/cultivars for buffering the effects of ever changing virulent pathogens and crop growth environments.

Chromsome and pedigree analysis of congenital malformation of external and middle ear

Objective:Using chromosome analysis of a Chinese pedigree to investigate the genetic relationship between chromosome and congenital malformation of the external and middle ear combined with pre-auricular fistula.Methods: Clinical data of all members from 3 family with congenital malformation of the external and middle ear combined with pre-auricular fistula were collected. A pedigrees chart of each family was draw Venous blood samples of all participants were taken for karyotype analysis.Results: A total of 21 members in three generations from three families were screened. Chromosomal abnormalities were detected in 9 people, including 3 patients and 6 carriers. The carriers were fathers and paternal grandparents. Structural abnormalities in chromosomes 1, 2 and 11 were identified.Conclusion:The genetic patterns of congenital malformation of the external and middle ear combined with the pre- auricular fistula in these three families are consistent with autosomal recessive inheritance. Family survey is helpful for further study of this disease.

A Pedigree Analysis of a Family With Familial Hypercholesterolemia

Objective The current study was designed to investigate the features of a family with familial hypercholesterolemia(FH). Methods Twenty members of three generations in a family with FH were enrolled in the study. The data collected were from clinical observation and subjected to pedigree analysis. Results The proband was a 41 years old male who suffered from angina pectoris with multi-vessel stenosis of coronary artery at the age of 40. Among 20 members, 8 individuals were demonstrated with hypercholes-terolemia in this family with the total incidence of 40% [54.5% (6/11) in male and 22. 2% (2/9) in femaleThe serum total cholesterol level was elevated in childhood from 7. 1 to 10. 8 mmol/L and tended to be raised with increasing age. In addition, the level of total cholesterol was found to be elevated both in a monozy-gote twin brothers and their offspring in the family. Conclusion FH appears to be a hereditary disease of autosomal dominance inheritance and the outcome of FH patients with coronary heart disease seems to be poor in prognosis.

Pedigree analysis of nationally approved soybean cultivars from 1984 to 2013 and implications for breeding

To reveal origins of 316 state authorized varieties from 1984 to 2013, rules of their parentsJ selection including types and hybrid configurations of direct parents, geo-graphical sources and types of their ancestors were analyzed. Various important direct parents and ancestors were summarized and nuclear contribution of ancestors was also estimated by pedigree analysis. Among 316 registered cultivars, 298 （94.3%） were bred by hybridization, and most of their direct parents were cultivars or breeding lines （65.5%）. Cultivars and breeding lines were mostly used as female parents, with 53.0% and 38.7% respectively. The 316 released cultivars were traced to 373 final ancestors, mainly com-posed of landraces （55.5%） and breeding lines （36.7%）. The 373 final ancestors came from different regions, including 121 from northern area, 110 from Huang-Huai-Hai area, 53 from southern area and 76 from abroad. These ancestors were mainly from the same ecologic zone as the approved cultivars. Newly approved cultivars always have more ancestors and a broader genetic base. However, distribution of these ancestors was unbalanced, and a few ancestors provided significant genetic contributions to later generations, such as the most concentrated final ancestors from Huang-Huai-Hai region followed by northern and southern regions. These results offer more information regarding their important parents and provide valuable references to soybean breeding. We should increase soybean germplasm exchanges with different regions and make use of elite lines, foreign cultivars and wild soybean germplasm to broaden the genetic background.

Genetic Diversity and Ancestral History of the German Angler and the Red-and-White Dual-Purpose Cattle Breeds Assessed through Pedigree Analysis

Local cattle breeds continue to decline in numbers partly due to the use of high performing breeds in advanced production systems where genetic material of elite animals is widely spread. The objective of this study was to assess the within and across breed genetic diversity of the Angler and Red-and-White dual-purpose (DP) cattle breeds applying different inbreeding concepts. Classical and ancestral inbreeding coefficients were computed from pedigree data using the gene dropping method. Effective population size was calculated based on the increase of classical inbreeding, and based on ancestral inbreeding to obtain what was termed as ancestral effective population size. Furthermore, the effective number of founders and ancestors were computed to assess the disequilibrium of founder contribution in the reference populations. The analyses were performed separately for each breed and for a combined dataset. The Angler pedigree was more complete (88%) in the first parental generation but completeness declined with increasing pedigree depth. Average classical inbreeding coefficients of inbred individuals were 2.19%, 1.94% and 2.07%, while average Ballou’s ancestral inbreeding coefficients were 3.69%, 1.39% and 2.21% for the Angler, Red-and-White DP and the combined breed pedigree analyses, respectively. Ancestral history coefficient is a novel coefficient and its estimates were similar and strongly correlated to Ballou’s coefficients (r = 0.99, p < 0.001). The effective population size estimates ranged from 156 to 170 for the classical inbreeding based method, and as low as from 50 to 54 for the ancestral history coefficient based method. The effective number of founders and ancestors ranged from 310 to 532, and 90 to 189, respectively. Our results show that the Red Holstein breed is a key progenitor of the breed populations under study. This highlights cross breeding schemes introduced to improve the milk trait performance of the Angler and Red-and-White DP breeds some decades ago.

RET proto-oncogene mutation analysis in a pedigree with multiple endocrine neoplasia 2A

Objective To discuss clinical diagnosis and treatment of multiple endocrine neoplasia ( MEN) 2A,and report the mutation of RET proto-oncogene in a pedigree of three patients with MEN 2A. Methods Bilateral adrenalectomy was performed on two of the three

Resulting of pedigree and topology of centripetal spatial schema in Chinese traditional cities

Chinese Traditional Maps and Local Chronicles serve as significant sources for investigating the urban history of ancient Chinese cities.These documents prioritize the abstract representation of topological relationships over precise numerical values and geometric shapes.This is consistent with the traditional Chinese city image and spatial schema emphasizing“harmony between man and nature”.Most Chinese Traditional Maps reflect a centripetal spatial schema,wherein the core area is located at the center,and other locations are positioned hierarchically about the center.Based on this data,this research aims to categorize and examine the development and evolution of the centripetal spatial schema in ancient Chinese cities by constructing a pedigree of types.The authors identify three types and summarize their causes,calculate the topological features,and reveal their correlations with the type of pedigree.This study reveals that cities with different centripetal forms exhibit regular differences in the accessibility,centrality,and functional attributes of central nodes,as well as the proportion of nodes with different attributes in the city.Overall,the conclusion aims to deepen people’s understanding of traditional Chinese spatial concepts at the macro-urban level,particularly in the context of China’s current urban renewal wave.Additionally,it provides practical references for inheriting and applying Chinese traditional construction wisdom.