Sib Families Research Articles

Evaluation of genetic parameters of growth traits in G2 selected generation of Penaeus monodon

Fifteen whole sib families of the second-generation Penaeus monodon were constructed using artificial mating design in 2020. After labeling the families with fluorescent markers, the growth traits and genetic parameters were evaluated in a cement pond for 56 days. The results showed that the coefficient of variation of growth traits was 11.52-47.53%, indicating a high genetic variation. The heritability range of growth traits of the G2 population of P. monodon was 0.25±0.03-0.41±0.13, which belonged to medium and high heritability, and the statistical test results were significant (P<0.01). The heritability of body length and body weight were 0.38±0.11 and 0.41±0.13, respectively. The evaluation results of genetic correlation among growth traits were highly positive, and the statistical test results were significant (P<0.01). The genetic correlation between body weight and body length was the highest (0.99), and the genetic correlation between the width of the first carapace and the height of the first abdominal segment was the lowest (0.71). The phenotypic correlation between body weight and body length was the highest (0.93), and the lowest was head breastplate width and first abdominal segment height (0.53). These results showed that the G2 generation population of P. monodon has high genetic improvement potential, and the combination of family selection and individual selection achieved better genetic gain. The growth traits were highly positively correlated. Body length and body weight could be selected as the key traits for fast growth line selection, while the other growth traits could be indirectly selected through positive genetic correlation.

Identification of three large full-sib families of Quercus rubra for genetic mapping in an isolated planting outside the species’ range in Germany

Abstract Forest tree breeding faces challenges due to long generation times and high costs. To address these issues, the concept of “breeding without breeding” (BwB) offers the opportunity to accelerate breeding cycles by using naturally generated half- sib and full-sib families. An isolated population of trees may provide an ideal environment to identify full-sib families for genetic mapping without the need for controlled pollination. In this study, paternity analysis based on genotyping of 16 SSR markers in 1232 seedlings identified three large full-sib families of Quercus rubra (Qr_N - Qr_W with 576 siblings, Qr_N - Qr_S with 175 siblings and 124 siblings in the family Qr_P - Qr_11). Paternity assignments were effectively corroborated by segregation analysis, resulting in large F1 full-sib families for further experiments such as Quantitative Trait Locus (QTL) mapping.

Additive and non-additive genetic variance in juvenile Sitka spruce (Picea sitchensis Bong. Carr)

Many quantitative genetic models assume that all genetic variation is additive because of a lack of data with sufficient structure and quality to determine the relative contribution of additive and non-additive variation. Here the fractions of additive (fa) and non-additive (fd) genetic variation were estimated in Sitka spruce for height, bud burst and pilodyn penetration depth. Approximately 1500 offspring were produced in each of three sib families and clonally replicated across three geographically diverse sites. Genotypes from 1525 offspring from all three families were obtained by RADseq, followed by imputation using 1630 loci segregating in all families and mapped using the newly developed linkage map of Sitka spruce. The analyses employed a new approach for estimating fa and fd, which combined all available genotypic and phenotypic data with spatial modelling for each trait and site. The consensus estimate for fa increased with age for height from 0.58 at 2 years to 0.75 at 11 years, with only small overlap in 95% support intervals (I95). The estimated fa for bud burst was 0.83 (I95=[0.78, 0.90]) and 0.84 (I95=[0.77, 0.92]) for pilodyn depth. Overall, there was no evidence of family heterogeneity for height or bud burst, or site heterogeneity for pilodyn depth, and no evidence of inbreeding depression associated with genomic homozygosity, expected if dominance variance was the major component of non-additive variance. The results offer no support for the development of sublines for crossing within the species. The models give new opportunities to assess more accurately the scale of non-additive variation.

Water Requirement and Efficacy of a Prototype Hatchery for Selective Breeding of Rohu, <i>Labeo rohita</i>

A prototype hatchery was constructed at Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, India to produce spawn of fullsib families of rohu (Labeo rohita) carp and mass production of genetically improved rohu spawn. While following combined selection method, fullsib families have to be produced and reared separately from fertilized eggs to fingerlings i.e., till taggable size for individual tagging. The specialized hatchery was developed for individual fullsib family spawn production i.e., fertilized eggs to spawn. Water requirement study was performed for full sib family production as well as for mass scale spawn production and, it was worked out to be 10.54 and 81.07 m3 for one fullsib family and a million of spawn production, respectively. The specialized hatchery improved the production of fullsib families and spawn recovery percentage to a greater extent. Recovery of fullsib families increased from 70-82% to 94-100% in different year classes. In the present paper, efficacy of the hatchery for fullsib family and mass scale spawn production in selective breeding programme of rohu for last 19 years is discussed. The same model of hatchery can also be utilized for selective breeding programme for any other carp species.

Elucidation and characterization of QTLs for Russet formation on apple fruit in ‘Honeycrisp’-derived breeding germplasm

Russet formation in apples (Malus domestica Borkh.) is a superficial skin disorder that detracts from fruit appearance and therefore is a breeding target in many apple scion breeding programs. Previous studies have reported quantitative trait loci (QTLs) for russet formation, but these results have been limited to a narrow genetic background, which reduces breeding utility. In this study, 14 breeding parents were represented in 13-full sib families, nine of which were ‘Honeycrisp’-derived while the other four were derived from ‘Minneiska’, an offspring of ‘Honeycrisp.’ Two previously reported QTLs, on linkage group (LG) 2 and LG6, were confirmed and characterized for the first time in ‘Honeycrisp’-derived germplasm. Five other putative QTLs were also detected. The QTLs characterized in this study could be targeted for DNA test development to be used in marker-assisted selection. Non-additive interactions were observed at and between the LG2 and LG6 QTLs. Future work should include validation of QTL and haplotype effects in other germplasm, development of trait-predictive DNA tests for use in apple breeding programs, and exploration of genome-wide prediction models for russet formation.

Recurrent selection of new breeding lines and yield potential, nutrient profile and in vitro rumen characteristics of Melilotus officinalis

Melilotus officinalis is an important forage and green manure crop. There is a high degree of genetic diversity within species of M. officinalis . Despite the forage potential and the ability of nitrogen fixation, it has not been propagated in recent years because its high coumarin content. As a forage crop, the breeding goal of M. officinalis was mainly focused on improving forage yield and quality and reducing coumarin content. In this study, 25 superior half sib (HS) families of M. officinalis were used to carry out the second cycle recurrent selection, and genotypic variation of key traits (yield, quality and coumarin content) at two locations during 2018 and 2019 seasons were evaluated. Significant genotypic variation existed for the key traits: plant height (PH), dry biomass (DB), crude protein (CP), acid detergent fiber, neutral detergent fiber and coumarin. Also, significant genotype × location interactions were observed for the traits: DB, PH, CP, stem diameter, acid detergent lignin and acid insoluble ash ( P < 0.05). Coumarin was negatively correlated with DB and PH, and positively correlated with CP. Genetic gain of all the traits of the second cycle recurrent selection were lower than that of the first cycle recurrent selection, except for PH and leaf/stem ratio (LSR). After the second cycle recurrent selection, the genetic gains of coumarin and LSR were higher than for other traits. Furthermore, new breeding lines generated by polycrossing superior HS families were evaluated. The polycrossing improved the yield and in vitro rumen fermentation characteristics and reduced the coumarin content. Our work provides new breeding lines of M. officinalis, beneficial for a sustainable grassland-based livestock industry. • Genotype × environment interactions affect yield and quality traits. • Recurrent selection process is useful to obtain plant materials with low coumarin content and high yield. • Superiority of new M. officinalis lines over currently grown demonstrated on fields and in vitro rumen fermentation. • We developed new breeding lines of M. officinalis beneficial for livestock industry.

Genetic parameters and selection in full-sib families of tall fescue using best linear unbiased prediction (BLUP) analysis

BackgroundBetter understanding of genetic structure of economic traits is crucial for identification and selection of superior genotypes in specific breeding programs. Best linear unbiased prediction (BLUP) is the most efficient method in this regard, which is poorly used in forage plant breeding. The present study aimed to assess genetic variation, estimate genetic parameters, and predict breeding values of five essential traits in full sib families (recognized by EST-SSR markers) of tall fescue using REML/BLUP procedure.MethodForty-two full-sib families of tall fescue (included of 120 individual genotypes), recognized by EST-SSR markers along with twenty-one their corresponding parental genotypes were assessed for biomass production and agro-morphological traits at three harvests (spring, summer, and autumn) in the field during 4 years (2017–2020).ResultsConsiderable genotypic variability was observed for all traits. Low narrow-sense heritability (h2n) for dry forage yield (DFY) at three harvest indicates that non-additive gene actions may play an important role in the inheritance of this trait. Higher h2n of yield related traits and flowering time and also significant genetic correlation of these traits with forage yield, suggests that selection based on these traits may lead to indirect genetic improvement of DFY.ConclusionOur results showed the adequacy of REML/BLUP procedure for identification and selection of preferable parental genotypes and progenies with higher breeding values for future breeding programs such as variety development in tall fescue. Parental genotypes 21 M, 1 M, and 20 L were identified as superior and stable genotypes and could also produce the best hybrid combinations when they were mostly used as maternal parent.

Comparison Of Growth Of Organic Tilapia From Selective Breeding Program, Fed With Organic Pellet Feed and Duckweed Under The Biofloc Farming System

This study was conducted to compare the growth performance of organic tilapia from the selective breeding program, fed with organic pellet feed and duckweed under the biofloc farming system. A total of 100 full sib families with stocking weight 20.2 (7.54) g was randomly separated from each family and divided into two groups. Each group was stocked in four separates 2m by 2m by 1m cages, the cages were hanged in 64 m3 P.E. tank under biofloc system. The first group was fed with organic pellets (34% protein feed), for 4 replicates in the same tank. Another group was fed with duckweed, for 4 replicates in another same tank. After two months of rearing, the growths of organic tilapia from the selective breeding program fed with organic pellet feed and duckweed under the biofloc farming system were not significantly different (p>0.05) for both total weight and length. The total weight and length of organic tilapia fed with duckweed and organic pellet feed were 29.47 (23.55) and 29.09 (23.67) g, respectively. The main finding of the present study is that the duckweed can be used in a selective breeding program of Nile tilapia without altering the relative performance of the families. This finding is of benefit since it justifies the current trends of organic tilapia production.

Prediction ability of genome-wide markers in Pinus taeda L. within and between population is affected by relatedness to the training population and trait genetic architecture.

Genomic prediction has the potential to significantly increase the rate of genetic gain in tree breeding programs. In this study, a clonally replicated population (n = 2063) was used to train a genomic prediction model. The model was validated both within the training population and in a separate population (n = 451). The prediction abilities from random (20% vs 80%) cross validation within the training population were 0.56 and 0.78 for height and stem form, respectively. Removal of all full-sib relatives within the training population resulted in ∼50% reduction in their genomic prediction ability for both traits. The average prediction ability for all 451 individual trees was 0.29 for height and 0.57 for stem form. The degree of genetic linkage (full-sib family, half sib family, unrelated) between the training and validation sets had a strong impact on prediction ability for stem form but not for height. A dominant dwarfing allele, the first to be reported in a conifer species, was discovered via genome-wide association studies on linkage Group 5 that conferred a 0.33-m mean height reduction. However, the QTL was family specific. The rapid decay of linkage disequilibrium, large genome size, and inconsistencies in marker-QTL linkage phase suggest that large, diverse training populations are needed for genomic selection in Pinus taeda L.

Identification of markers for functional traits in Murrah buffaloes

Twelve half sib families were created and two functional traits, viz. age at first heat and age at first calving were recorded for 4,851 and 946 daughters belonging to 12 sires. Partial genome scan was carried out using Interval Mapping with different algorithms. The QTLs obtained for each half sib family were further subjected to meta analysis to identify chromosomal regions associated with age at first heat and age at first calving on 8 chromosomes of buffalo. We identified 4 metaQTL regions on chromosomes BBU1q, BBU6, BBU7, BBU8 and BBU10; 3 metaQTL regions on BBU2q; 2 metaQTL regions on BBU9 and one on BBU15 of buffalo. Comparative genomics was used for finding out genes underlying the meta-QTL regions. 1019 genes were found to be underlying the metaQTL regions in buffaloes assuming buffalo-cattle-human synteny. Several of these genes are supposedly important candidate genes for further analysis as several of them revealed functions related to fertility. The QTL markers identified in the present analysis can be used in the breeding programs of buffalo to select the bulls which affect the functional traits and thus reduce the cost of production.

QTL × environment interactions underlie ionome divergence in switchgrass.

Ionomics measures elemental concentrations in biological organisms and provides a snapshot of physiology under different conditions. In this study, we evaluate genetic variation of the ionome in outbred, perennial switchgrass in three environments across the species’ native range, and explore patterns of genotype-by-environment interactions. We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens. Concentrations of 18 mineral elements were determined in whole post-anthesis tillers using ion coupled plasma mass spectrometry (ICP-MS). These measurements were used to identify quantitative trait loci (QTL) with and without QTL-by-environment interactions (QTLxE) using a multi-environment QTL mapping approach. We found that element concentrations varied significantly both within and between switchgrass ecotypes, and GxE was present at both the trait and QTL level. Concentrations of 14 of the 18 elements were under some genetic control, and 77 QTL were detected for these elements. Seventy-four percent of QTL colocalized multiple elements, half of QTL exhibited significant QTLxE, and roughly equal numbers of QTL had significant differences in magnitude and sign of their effects across environments. The switchgrass ionome is under moderate genetic control and by loci with highly variable effects across environments.

Environmental effects on the ontogenesis of tadpole personality

Behaviours are highly plastic phenotypic traits whose variation depends on the short-term response to external stimuli (contextual plasticity) and on the long-term response to past experiences (developmental plasticity). Despite this great flexibility, behaviours often show individual differences that are consistent across time and context (i.e. ‘animal personality’). By adopting a behavioural-reaction-norm (BRN) approach, we used a factorial common garden experiment to investigate the effects of contextual and developmental plasticity on the antipredator behaviour of treefrog tadpoles, Hyla intermedia . We raised 96 tadpoles from eight half sib–full sib families under different biotic (predation risk) and abiotic (shading) environmental conditions and described their activity and spatial behaviour in experimental arenas with either a caged predator, a caged conspecific or an empty cage. Tadpoles raised with predator cues were always less active and stayed further away from caged predators than their predator-naïve siblings. Tadpoles raised in the shade were less active than those raised in the sun. Not only was the raising environment responsible for among-individual variation but it also acted at the within-individual level by affecting behavioural repeatability, which was higher in predator-naïve than in predator-experienced tadpoles. Besides the important role of the environment, this study also shows consistent variation in BRNs with body size and time: tadpoles became more active as they got larger and their activity increased with time in the presence of caged predators, decreased in the presence of empty cages and did not change with caged conspecifics. These results suggest that the effects of past and present experiences on tadpole behaviour vary with time as a consequence of growth and development. • We investigate the environmental effects on the development of tadpole behaviour. • Tadpoles were raised under different predation risk and shady conditions. • The ontogenetic environment has strong effects on tadpole personality. • Stressful environments reduce variation in personality. • Independent of the environment, personality changes during growth and development.

Genetic Gains to Grain Yield of Maize Varieties for Small Farmers in Brazil

The demand for expanding the genetic base in working collections of older maize breeding programs points to the need to pool efforts and reaffirm methodologies for conserving genetic variability that can still be accessed in maize populations. The objective of the work was to select full sib maize progenies and to estimate genetic gains in the first cycle of reciprocal recurrent selection for common maize intended for cultivation in a region characterized by family farm, in Brazil. We evaluated 120 full sib families of maize from crossbreeding between individuals of the Cimmyt and Piranão varieties. Competition trials were conducted at two experimental stations in the state of Espírito Santo, Brazil. A randomized block design was adopted with 2 repetitions, arranged in sets. Different selection indexes were tested in order to enhance gains in productivity and prolificacy. The selection of 40 superior families made it possible to estimate a gain of 0.77 Mg ha-1 in grain productivity for producers in the region. With these results, we discussed the importance of work to improve maize populations for small producers to motivate the conservation of the genetic variability of tropical maize germplasm. Thus, from the results obtained in this study, we show the possibility of investing in technologies aimed at small producers in order to motive the conservation of genetic resources, food sovereignty of producers and, consequently, world security, given the importance of this culture for human feed.

Changes of genetic variances and heritability by effect of selection in a Mexican local variety of Squash

A local variety of squash (Cucurbita pepo L.), ‘Round Zuchinni’ type from Los Reyes Acatlixhuayan State of México, México, was simultaneously evaluated and selected. The objective was to study effect of selection on genetic variance and heritability. Additive genetic variance decreased in seven of nine traits studied: fruit height (79.93 %); fruit weight (65.72 %); fruit width (60.91 %); flesh thickness (57.66 %); flesh color (43.70 %); dry weight of seed (39.54 %); flesh flavor (16.60 %); except in width and seed length traits where it increased 63.40 % and 0.81 %, respectively. Only weight of seed had dominance genetic variance. The coefficient of additive genetic variance (CVA) fluctuated from 9.4 to 61.7 % in the first cycle, and from 9.4 to 51.8 % in the second cycle of selection-evaluation among traits. Heritability diminished in seven from nine characters. In general, the estimated genetic variances (additive and dominance) and heritability decreased as a result of combined selection of falf sib families.

Genotype by environment interactions for inner shell color and growth traits in the purple freshwater pearl mussel, Hyriopsis cumingii, reared with different water depths and mud substrates

A breeding selection program for improving inner shell color and growth was developed for Hyriopsis cumingii, to enhance purple pearl production. In freshwater pearl culture, adjusting culture water depth and mud substrate supply are routinely carried out to improve pearl quality. To improve selection decisions in different conditions, we estimated heritabilities and genotype by environment (G × E) interactions on inner shell color and growth traits in 1571 17-month-old animals from 8 half sib family of purple selective strain of H. cumingii reared in different water depths (WD1, 32 cm; WD2, 48 cm) and mud substrates (MS, mussel pond mud substrate; SS, shrimp pond mud substrate) were analyzed. With the same mud substrate, H. cumingii reared at WD1 showed increased performance in shell color and growth. Heritability estimates for growth traits (shell length, shell height, shell width, body weight and shell weight) were higher at WD1 and higher at WD2 for inner shell color parameters (L, a, band dE⁎) when rearing in MS, while showed opposite pattern in SS. At the same water depth, H. cumingii reared with MS showed better performance in shell color and growth traits. Heritability estimates for growth traits were higher in SS and higher in MS for inner shell color parameters when rearing at WD1, while showed opposite pattern at WD2. Heritability estimates for L, a and all growth traits were moderate and high (h2 > 0.15), while were low for b and dE⁎ (h2 < 0.15). Genetic correlations for inner shell color parameters and growth traits within the four conditions were less than 0.8, except that some combinations of depth and mud substrate with over 0.9 for shell growth traits and shell color traits showed significant G × E correlations. The rank of individuals with comprehensive breeding value was different in four conditions, and the percentage of individual family sources shared in some pair conditions were small, which indicated re-ranking during selective breeding program. This study provides guidelines for a selective breeding strategy for improving inner shell color and growth in H. cumingii when mussels are reared under different conditions

Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus).

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, FST estimates among the families of year class 2017 ranged between 0.009 – 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program.

Variability in Forage yield of a Silage Maize “Zea mays, L.”Base Population via Two Types of Families

The base population for the recent study which is ayellow seed synthetic variety of maize was provided by Dr. M. Abd El-Sattar Ahmed, professor of crop science, Crop Science Department, faculty of Agriculture, Egypt.Two types of families had formulated, as a step before selection for high yielding ability. Those were half-sib (H.S) fami-lies and the first generation of self-pollination(S1) families. Variability in the base population gene pool had estimated depending on variance components of the families. The ratio of σ2A/ σ2G indicated that, additive genetic variance was more effective in controlling green and dry forage yield. This might indicate the importance of additive genetic vari-ance in maize population, consequently, selection among inbred- progeny would expect to be superior to other meth-ods under most genetic situations. Reduction in mean values of forage yield associated with selfing, reached 0.62 and 0.57 for green forage yield (Kg/ plot) and dry forage yield (Kg/plot), respectively. Values of genotypic variances estimated from S1 families were of larger magnitude amounted to 1.63 and 1.94 times the corresponding values for half- sib families in green forage yield and dry forage yield. Opposite to that, environmental variance estimates from S1 families were 0.56 and 0.55 of the respective values from half- sib families in green forage yield and dry forage yield respectively.Genotypic variations in term of coefficient relative to the overall mean of green yield and dry yield were less than 20%of the character mean when estimated from half-sib and S1 families (10.85 vs. 13.96 and 10.21 vs. 14.31% for green and dry forage, respectively).Dry forage yield expressed the highest estimates of heritability in both family types (0.829 and 0.877 for half –sib and S1 families, respectively). While, the obtained values for green forage yield were of lower magnitude (0.53 and 0.67 for half-sib and S1 families, respectively). This might indicate addition-al environmental influences with green forage yield.

Phenotypic Variation in Climate-Associated Traits of Red Spruce (Picea rubens Sarg.) along Elevation Gradients in the Southern Appalachian Mountains

Red spruce (Picea rubens) is a long-lived tree species that thrives in cool, moist environs. Its ability to adapt to rapidly changing climate is uncertain. In the southern Appalachian Mountains, red spruce reaches its greatest abundance at high elevations, but can also occur across a range of mid and lower elevations, suggesting the possibility of a correlation between genetic variation and habitat. To assess clinal phenotypic variation in functional traits related to climate adaptation, we collected seed from 82 maternal sib families located along replicated elevational gradients in the Great Smoky Mountains National Park, TN (GSMNP) and Mount Mitchell State Park, NC (MMSP). The percentage of filled seeds and seed mass increased with elevation, indicating that successful pollination and seed development was greatest at the highest elevations. Seedlings sourced from GSMNP displayed a strong relationship between elevation and bud set when grown under common garden conditions. High elevation families set bud as many as 10 days earlier than low elevation families, indicating adaptation to local climate. Across parks, no effect of elevation was noted for bud flush. Our results demonstrate that red spruce in the southern Appalachian Mountains displays clinal variation in bud set that may reflect local adaptation to climate, although this varied between the two parks sampled. We suggest that genetic adaption of red spruce to different climate regimes, at both local and broad spatial scales, is in need of more intensive study, and should be carefully considered when selecting seed sources for restoration.

Evaluation of Seedling Seed Orchard of Grewia optiva Drummond for Morphometric and Fodder Quality Parameters

Forty half sib progenies in open pollinated seedling seed orchard of Grewia optiva Drummond were evaluated for morphometric and fodder quality traits. The analysis of variance indicated highly significant differences among the various half sib families for all the traits. The experimental results revealed that out of 40 families, ten families viz., SI-15, SO-3, HA-2, HA-3,HA-4,SO-7,SH-7,SO-4,SI-6 and SI-14 were found superior on the basis of overall mean performance for all quantitative and qualitative traits under study. Hence, these ten half sib families in the seedling seed orchard can be used in further breeding programme and providing mother’s replica.

Identification of QTLs for low somatic cell count in Murrah buffaloes

Mastitis, the most frequent and costly disease in buffalo, is the major cause of morbidity. The somatic cell count, an indirect indicator of susceptibility/resistance to mastitis, is a low heritable trait and thus a perfect candidate for marker assisted selection. Half sib families (12) were created and the somatic cell count was recorded at 3 stages of lactation during the first lactation of the 2,422 daughters belonging to 12 sires. Partial genome scan was carried out using interval mapping with different algorithms. The QTLs obtained for each half sib family were further subjected to meta analysis to identify chromosomal regions associated with somatic cell count on 8 chromosomes of buffalo. Four metaQTL regions were identified on chromosomes BBU1q, BBU8, and BBU10; 3 metaQTL regions on BBU2q, BBU9 and BBU15; 2 metaQTL regions on BBU6 and 1 on BBU7 of buffalo. Comparative genomics was used for finding out genes underlying the metaQTL regions; 1,065 genes were underlying the metaQTL regions in buffaloes assuming buffalo–cattle–human synteny. Genes (78) mapped to immune response. These genes are supposedly important candidate genes for further analysis. Gene ontology and network analysis was carried out on these genes. The genes identified belonged to immune response and defense mechanism. The QTL markers identified in the present analysis can be used in the breeding programs of buffalo to select the bulls, which are less susceptible to mastitis.