scholarly journals PEDIGREE ANALYSIS OF 222 ALMOND GENOTYPES REVEALS TWO WORLD MAINSTREAM BREEDING LINES BASED ON ONLY THREE DIFFERENT CULTIVARS

2020 ◽  
Author(s):  
Felipe Pérez de los Cobos ◽  
Pedro J. Martínez-García ◽  
Agustí Romero ◽  
Xavier Miarnau ◽  
Iban Eduardo ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Critical Role ◽  
Inbreeding Coefficient ◽  
Genetic Contribution ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Inbreeding Coefficients ◽  
Geographical Regions ◽  
The Usa ◽  
The Mean

ABSTRACTLoss of genetic variability is a steadily increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. High-quality pedigree data of 222 almond [Prunus dulcis (Miller) D.A. Webb, syn. P. amygdalus (L) Batsch] cultivars and breeding selections were used to study global genetic variability in modern breeding programs from Argentina, Australia, France, Greece, Israel, Italy, Russia, Spain and the USA. Inbreeding coefficients, pairwise relatedness and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars from two different geographical regions: ‘Tuono’-‘Cristomorto’ (local landraces from Puglia, Italy) and ‘Nonpareil’ (chance seedling selected in California, USA, from French original stock). Direct descendants from ‘Tuono’ or ‘Cristomorto’ number 75 (sharing 30 descendants), while ‘Nonpareil’ has 72 direct descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.036, with 13 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from the USA, France and Spain showed inbreeding coefficients of 0.067, 0.050 and 0.034, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain and Australia, trace back to six, five, four, four and two main founding genotypes respectively. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.133, with ‘Tuono’ as the main founding genotype (23.75% of total genetic contribution). Increasing as well as preserving current genetic variability is required in almond breeding programs worldwide to assure genetic gain and continuing breeding progress. Breeding objectives, apart from high and efficient productivity, should include disease resistance and adaptation to climate change. Ultimately, any new commercial almond cultivar has to be economically viable and breeders play a critical role in achieving this goal.

scholarly journals Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Felipe Pérez de los Cobos ◽  
Pedro J. Martínez-García ◽  
Agustí Romero ◽  
Xavier Miarnau ◽  
Iban Eduardo ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Tree Breeding ◽  
Inbreeding Coefficient ◽  
Genetic Contribution ◽  
Pedigree Data ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Inbreeding Coefficients ◽  
The Usa ◽  
The Mean

AbstractLoss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.

scholarly journals Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.)

2021 ◽  
Author(s):  
Amber Bassett ◽  
Kelvin Kamfwa ◽  
Daniel Ambachew ◽  
Karen Cichy
Keyword(s):  
Genetic Variability ◽  
Seed Coat ◽  
Principal Component ◽  
Breeding Programs ◽  
Flavor Intensity ◽  
Genome Wide ◽  
White Bean ◽  
The Usa ◽  
New Varieties ◽  
End Use

Abstract Key message Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture. Abstract Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown in three locations, and cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Extensive variation in sensory attributes was found across and within seed types. A set of genotypes was identified that exhibit extreme attribute intensities generally stable across all three environments. seed-coat perception and total flavor intensity had the highest broad-sense heritability (0.39 and 0.38, respectively), while earthy and vegetative intensities exhibited the lowest (0.14 and 0.15, respectively). Starchy and sweet flavors were positively correlated and highest in white bean genotypes according to principal component analysis. SNPs associated with total flavor intensity (six SNPs across three chromosomes), beany (five SNPs across four chromosomes), earthy (three SNPs across two chromosomes), starchy (one SNP), bitter (one SNP), seed-coat perception (three SNPs across two chromosomes), and cotyledon texture (two SNPs across two chromosomes) were detected. These findings lay a foundation for incorporating flavor and texture in breeding programs for the development of new varieties that entice growers, consumers, and product developers alike.

scholarly journals Population structure of Czech cold-blooded breeds of horses

2011 ◽  
Vol 54 (1) ◽  
pp. 1-9
Author(s):  
L. Vostrý ◽  
Z. Čapková ◽  
J. Přibyl ◽  
B. Hofmanová ◽  
H. Vostrá Vydrová ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Czech Republic ◽  
Generation Interval ◽  
Average Value ◽  
Inbreeding Coefficients

Abstract. In order to estimate effective population size, generation interval and the development of inbreeding coefficients (Fx) in three original breeds of cold-blooded horses kept in the Czech Republic: Silesian Noriker (SN), Noriker (N) and Czech-Moravian Belgian horse (CMB) all animals of the particular breeds born from 1990 to 2007 were analysed. The average values of generation interval between parents and their offspring were: 8.53 in SN, 8.88 in N and 8.56 in CMB. Average values of effective population size were estimated to be: 86.3 in SN, 162.3 in N and 104.4 in CMB. The average values of inbreeding coefficient were 3.13 % in SN stallions and 3.39 % in SN mares, in the N breed 1.76 % and 1.26 % and in the CMB breed 3.84 % and 3.26 % respectively. Overall averages of Fx were: 3.23 %, 1.51 % and 3.55 % for the breeds SN, N and CMB. The average value of inbreeding coefficient Fx increased by 1.22 % in SN, by 0.35 % in N and by 1.01 % in CMB, respectively. This may lead to a reduction in genetic variability. Reduction in genetic variability could be either controlled in cooperation with corresponding populations of cold-blooded breeds in other European countries or controlled by number of sires used in population

scholarly journals IDENTITY COEFFICIENTS IN FINITE POPULATIONS. I. EVOLUTION OF IDENTITY COEFFICIENTS IN A RANDOM MATING DIPLOID DIOECIOUS POPULATION

Genetics ◽  
1977 ◽  
Vol 86 (3) ◽  
pp. 697-713
Author(s):  
C Chevalet ◽  
M Gillois ◽  
R F Nassar
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Random Mating ◽  
Matrix Multiplication ◽  
Inbred Lines ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Mean ◽  
Over Time

ABSTRACT Properties of identity relation between genes are discussed, and a derivation of recurrent equations of identity coefficients in a random mating, diploid dioecious population is presented. Computations are run by repeated matrix multiplication. Results show that for effective population size (Ne) larger than 16 and no mutation, a given identity coefficient at any time t can be expressed approximately as a function of (1—f), (1—f)3 and (1—f)6, where f is the mean inbreeding coefficient at time t. Tables are presented, for small Ne values and extreme sex ratios, showing the pattern of change in the identity coefficients over time. The pattern of evolution of identity coefficients is also presented and discussed with respect to N eu, where u is the mutation rate. Applications of these results to the evolution of genetic variability within and between inbred lines are discussed.

scholarly journals Testing the breeding strategy of Hungarian Bronze turkey strains for maintaining genetic diversity with microsatellites

2011 ◽  
Vol 54 (4) ◽  
pp. 419-429
Author(s):  
S. Kusza ◽  
S. Mihók ◽  
L. Czeglédi ◽  
A. Jávor ◽  
M. Árnyasi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mating System ◽  
Breeding Strategy ◽  
Shannon Index ◽  
Inbreeding Coefficient ◽  
Control Population ◽  
Conservation Strategies ◽  
The Mean ◽  
Two Populations

Abstract. The aim of the study was to provide information on the genetic variability of the Hungarian Bronze turkey gene reserve population and its difference from the Broad-breasted turkey, and offer guidance and proposals for its future conservation strategies. Altogether, 239 Hungarian Bronze turkeys from 10 strains and 13 Broad-breasted turkeys as a control population were genotyped for 15 microsatellites. All loci were polymorphic with the average number of alleles per locus 3.20±1.146 in the Hungarian Bronze turkey. The mean expected (Hexp) and observed heterozygosity (Hobs) were not different (0.392 and 0.376, respectively) in the overall population, and similar values were obtained for hens and bucks and among hen strains. Inbreeding coefficient (FIS) and Shannon index (I) indicated that there was low inbreeding within hens and bucks. Our results confirm that the genetic diversity in the Hungarian Bronze turkey population has been preserved by the rotational mating system. Differences between the Hungarian Bronze turkey and the Broad-breasted turkey populations were determined. Nei’s unbiased values clearly indicated that the two populations are highly genetically differentiated.

scholarly journals PLUM VARIETIES USED AS PARENTS IN ROMANIAN BREEDING PROGRAM

2021 ◽  
Vol 37 (37) ◽  
pp. 6-13
Author(s):  
Mădălina Butac ◽  
Keyword(s):  
Genetic Diversity ◽  
Clonal Selection ◽  
Genetic Resistance ◽  
Inbreeding Coefficient ◽  
Prunus Domestica ◽  
Breeding Programs ◽  
The Mean ◽  
Coefficient Of Coancestry ◽  
Plum Varieties ◽  
Genetic Contributions

There are about three thousand varieties belonging to Prunus domestica available at present worldwide that can be used as genitors in plum breeding activity. An analysis of the pedigrees of plum cvs. developed in Romanian breeding programs shows that the most are descended from ‘Tuleu gras’, ‘Renclod Althan’, ‘Anna Späth’, ‘Stanley’ and ‘Early Rivers’, called 'ancestors'. That means the majority of plum cvs. have at least one of the ancestors as parent or grandparent. For those 40 plum cvs. registered in Romania in 60 years an increased number of crosses with these 'ancestors' has led to what we call 'inbreeding'. According to data presented in this paper, ‘Tuleu gras’ cv. was the most frequently used parent in the cross combinations, giving origin to 23 cvs. Among the other frequently used genitors were: ‘Renclod Althan’ (7 cvs.), ‘Anna Späth’ (3 cvs.) and ‘Stanley’ (1 cv.). Many of the cultivars – 32 altogether (80%) have originated from hybridization, whereas 4 cvs. have originated from open pollination, others 3 cvs. from mutagenesis and 1 cv. from clonal selection. The goal of this work is to measure genetic diversity presently use in Romanian plum breeding. Pedigrees of each cv. were used to study the genetic contributions of ancestor. Of the 40 cvs. analyzed, 33 had an inbreeding coefficient other than zero. The overall mean inbreeding coefficient was 0.419 for all cvs., where their parentages were known. For cvs. with unknown parentage (nonrelated with known parentage) the inbreeding coefficient is zero. The mean coefficient of coancestry of 40 plum cvs. are 0.081 with ‘Tuleu gras’ cv., 0.019 with ‘Renclod Althan’ and ‘Anna Späth’ cvs., 0.017 with ‘Early Rivers’ cv., 0.014 with ‘d’Agen’ and ‘Renclod Violet’ cvs. and 0.005 with Stanley cv. In conclusion, plum breeders have worked with populations of greatly reduced genetic diversity and this strategy becomes a problem because it leads to genetic impoverishment, and, also, the loss of the genetic resistance to different diseases.

scholarly journals Inbreeding, Coancestry, and Founding Clones of Almonds of California, Mediterranean Shores, and Russia

1994 ◽  
Vol 119 (6) ◽  
pp. 1279-1285 ◽  
Author(s):  
Ali Lansari ◽  
Dale E. Kester ◽  
Amy F. Iezzoni
Keyword(s):  
United States ◽  
Genetic Gain ◽  
Prunus Dulcis ◽  
The United States ◽  
Inbreeding Coefficient ◽  
Market Demand ◽  
Breeding Programs ◽  
Genetic Base ◽  
Trace Back ◽  
The Mean

The mean inbreeding and coancestry coefficients were calculated for almond, Prunus dulcis (Miller) D.A. Webb, cultivars from the United States, France, Spain, Israel, and Russia. To improve cultivars to meet market demand, the recurrent use of four selections as parents in U.S. breeding programs has resulted in a mean inbreeding coefficient (F) of 0.022 in this collection. In France, a single cultivar, Ferralise, has an inbreeding value of F = 0.250, while cultivars of other almond-producing countries are noninbred (F = 0). Due to the use of common parents, U.S., Russian, and Israeli cultivars share coancestry, while coancestries also exist between French and Spanish almond germplasm. Cultivars of known parentage in the United States, Russia, Israel, France, and Spain trace back, respectively, to nine, eight, three, four, and three founding clones. Future almond-breeding programs may narrow the genetic base and thereby limit genetic gain.

scholarly journals Pedigree structure of American bison (Bison bison) population

2018 ◽  
Vol 63 (No. 12) ◽  
pp. 507-517 ◽  
Author(s):  
E. Skotarczak ◽  
P. Ćwiertnia ◽  
T. Szwaczkowski
Keyword(s):  
Mean Value ◽  
Bison Bison ◽  
Pedigree Information ◽  
Effective Population ◽  
Pedigree Structure ◽  
Breeding Programs ◽  
Inbreeding Coefficients ◽  
Animal Populations ◽  
The Mean ◽  
Inbreeding Level

An effective realization of breeding programs in zoos is strongly determined by completeness of animal pedigree information. The knowledge of pedigree structure allows to maintain optimal genetic variability of a given population. The aim of this study was to estimate the parameters describing the pedigree structure of American bison housed in zoos in the context of further management of the population. Finally, 4269 American bison were analysed (1883 males, 2217 females, and 169 with unknown sex). The registered animals were born between years 1874 and 2013. The following pedigree parameters were estimated: number of fully traced generations, number of complete generations equivalent, index of pedigree completeness, individual inbreeding coefficients, increase of inbreeding for each individual, effective population size, and genetic diversity. The maximum number of fully traced generations was 3 (the mean value is 0.693). The mean inbreeding coefficient for the population studied was 3.26%, whereas individual increase in inbreeding ranged from 0 to 25.12%. Although the pedigree parameters (including the inbreeding level) in the American bison obtained in the present study seem to be acceptable (from the perspective of other wild animal populations), they can be over/underestimated due to incomplete pedigree.

scholarly journals Inbreeding in Pembroke Welsh Corgi Population in Poland

2015 ◽  
Vol 15 (4) ◽  
pp. 861-866 ◽  
Author(s):  
Wiesław Piotr Świderek ◽  
Katarzyna Fiszdon ◽  
Natalia Kacprzak
Keyword(s):  
Inbreeding Coefficient ◽  
Polish Population ◽  
Kennel Club ◽  
Inbreeding Coefficients ◽  
The Mean

Abstract The objective of this study was to determine changes in the coefficients of inbreeding for a comparatively new Polish population of Pembroke Welsh Corgis. Calculations were based on 780 pedigrees of dogs born between 1979 and 2010 and registered with the Polish Kennel Club. The mean inbreeding coefficients for animals born during those years varied from 0.4% to 8.93%. The lowest individual inbreeding coefficient was 0.06%, whereas the highest reached 25.1%.

scholarly journals Isoenzymatic variation in the germplasm of Brazilian races of maize (Zea mays L.)

2000 ◽  
Vol 23 (2) ◽  
pp. 375-380 ◽  
Author(s):  
Marcos Aparecido Gimenes ◽  
Catalina Romero Lopes
Keyword(s):  
Genetic Diversity ◽  
Zea Mays ◽  
Genetic Variability ◽  
Zea Mays L ◽  
Polymorphic Locus ◽  
Maize Breeding ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Total Genetic Diversity ◽  
The Mean

There are more than 200 races of maize (Zea mays L.) divided into three groups (ancient commercial races, the recent commercial races, and indigenous races). Although the indigenous races have no commercial value, they have many important characteristics which can be incorporated into maize breeding programs. Most Brazilian indigenous germplasm race stocks were collected at least 40 years ago, and nothing is known of the genetic variability present in this germplasm. The genetic variability was assayed in 15 populations from four indigenous races of maize (Caingang, Entrelaçado, Lenha and Moroti) and five indigenous cultivars, using five isoenzymatic systems encoded by 14 loci. The analysis revealed a low level of variability among the samples studied. Overall, the mean number of alleles/polymorphic locus was three, 64.3% of the loci analyzed being polymorphic and the estimated heterozygosity was 0.352. The mean number of alleles/polymorphic locus per population was 1.6. A mean of 47.5% of the loci were polymorphic. The mean expected heterozygosity was 0.195, the mean genetic identity was 0.821 and the proportion of total genetic diversity partitioned among populations (Gst) was 0.156. A founder effect could explain the low variability detected.

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