پديد آورندگان :
كريمي، كريم دانشگاه شهيد باهنر كرمان - دانشكده كشاورزي - گروه علوم دامي , اسماعيلي زاده كشكو.يه، علي دانشگاه شهيد باهنر كرمان - دانشكده كشاورزي - گروه علوم دامي , اسدي فوزي، مسعود دانشگاه شهيد باهنر كرمان - دانشكده كشاورزي - گروه علوم دامي
كليدواژه :
ژنوم گاو , عدم تعادل پيوستگي , گاو بومي فارس , نشانگرهاي چند شكل تك نوكلئوتيدي
چكيده فارسي :
زمينه مطالعاتي: شناسايي سطوح عدم تعادل پيوستگي در ميان جمعيت ها ابزاري مفيد در مطالعه تاريخچه جمعيت ها و شناسايي نواحي ژنومي مرتبط با صفات مهم اقتصادي است. هدف: در اين تحقيق، به منظور فراهم آوردن اطلاعات پايه مورد نياز در طراحي مطالعات ارتباطي كل ژنوم و بررسي تغييرات اندازه موثر جمعيت در گاوهاي بومي فارس، سطوح عدم تعادل پيوستگي در ژنوم افراد اين جمعيت مورد مطالعه قرار گرفت. روش كار: بدين منظور تعداد 10 راس از گاوهاي بومي فارس به طور تصادفي نمونه برداري شدند و به كمك تراشه Illumina Bovine HD در 777962 جايگاه SNP تعيين ژنوتيپ شدند. كنترل كيفي داده ها بر اساس نرخ فراخواني تعيين ژنوتيپ، انحراف از تعادل هادري–وينبرگ و فراواني آلل هاي نادر در جايگاه هاي مختلف انجام شد و 55718 جايگاه براي انجام آناليزهاي بعدي انتخاب شدند. كليه جفت مقايسه هاي بين SNPها در سه دسته فاصلهاي صفر تا 10، 10 تا 100 و 100 تا 1000 كيلوبازي تقسيم بندي شدند و متوسط آماره r2 براي تمامي كروموزوم هاي غيرجنسي در اين فواصل محاسبه شد. نتايج: متوسط r2 بالاتر از ۰/۳ در فواصل كمتر از Kb 9 و متوسط r2 بالاتر از ۰/۲ در فواصل كمتر از Kb 60 مشاهده گرديد. مقادير r2 بدست آمده در فواصل بين نشانگري كوتاه تر (كمتر از Kb 100) از اطمينان بيشتري برخوردار بودند. مقادير بالاي r2 يافت شده در اين مطالعه نشان دهنده سطح بالاي بروز هم خوني و كاهش شديد جمعيت موثر در گاوهاي بومي فارس است. نتيجه گيري نهايي: نتايج اين مطالعه ميتواند در تعيين تراكم نشانگري مورد نياز جهت كسب دقت كافي در مطالعات ژنومي احتمالي در گاوهاي بومي فارس به كار گرفته شود.
چكيده لاتين :
Introduction:
Knowledge on the extent of linkage disequilibrium (LD) among populations is a useful
tool to study the evolutionary history of populations and
to detect the genomic regions associated
with economically important traits. In recent years, high dense SNP data has been widely applying as
the standard tools in LD analysis of livestock populations. In the current study,
LD levels in the
genome of Fars
native cattle
were investigated in order to provide basic information required to design
genome
-
wide association studies and to survey on probable changes in the effective size of this
population.
Moreover, the applicability of the modern genomic technolo
gies such as genomic
selection can be evaluated using LD data.
Material
and methods:
Ten individuals were randomly sampled from Fars native cattle population
and were genotyped using Illumina Bovine HD beadchip for 777962 SNP markers. Data quality
control
was performed based on genotyping call rate, deviation from Hardy
-
Weinberg equilibrium
and minor allele frequency. Thereby, a total of 55,718 SNPs were remained for further analyses.
MAF was calculated using PLINK v1.07 for all autosomal SNPs and the dist
ribution of the allelic
frequencies was graphed as the proportion of SNPs represented in 6 different categories of MAF:
<0.05, ≥0.05 to <0.1, ≥0.1 to <0.2, ≥0.2 to <0.3, ≥0.3 to <0.4 and ≥0.4 to ≤0.5.
The measure of LD
(r
2
)
was
calculated for all marker pa
irs of each chromosome (syntenic SNPs) using the SnppldHD
software.
SNP pairwise comparisons were grouped in the three distance sets including zero to 10 Kb,
10 Kb to 100 Kb and 100 Kb to 1000 Kb intervals and average r
2
was computed for all of the
autosom
es at these distances. Results and
d
iscussion:
Number of SNPs located on X, Y, mitochondrial chromosomes and
unknown sites were respectively equal to 39367, 1224, 343 and 1735 and all of those were excluded
from further analysis.
Average distance between
adjacent SNPs was equal to 48.1 Kb and the average
of MAF was equal to 0.223. Also, 44.5% of sites had MAF < 0.2 and the highest proportion of SNPs
was observed at category with MAF 0.4 to 0.5. In this study, average r
2
at distances less than 1 Kb
was equa
l to 0.46. Moreover, average r
2
between SNPs with distances less than 10 Kb was equal to
0.35. Average r
2
values above 0.3 and 0.2 were observed at distances less than 9 Kb and 60 Kb,
respectively. Survey on LD decay in 10 to 100 Kb distances indicated tha
t based on 10 to 20 Kb SNP
bins, average r
2
changed from 0.294 to 0.365. The average r
2
values obtained at shorter distances (less
than 100 Kb) had higher reliabilities than those obtained at longer distances. The pattern of LD was
significantly different
among various chromosomes. LD decay in distances more than 400 Kb was
very slow and reached to a relatively stable level. Average r
2
decreased with increase in physical
distance between SNPs. However, change levels were not the same for different chromosom
es. This
can be attributed to different recombination rates and selection intense
s
between chromosomes.
Average r
2
for all chromosomes was equal to 0.118 and the highest level of r
2
was observed in
chromosome 17 (r
2
=0.153) and the lowest one was in
chromosome 26 (r
2
=0.093).
Change trend in
effective population size of Fars native cattle indicated that during 2000 to 5 previous generations,
effective population size was decreased from 3076 to 14 in this population.
Slower LD decay in more recent gener
ations indicated that this population has experienced a severe decline in recent
generations. Clearly, at this situation, design a conservation program is essential to avoid extinction
of Fars native cattle.
Markers density applied in this study (55,718) w
ill be appropriate to obtain
enough accuracy in genomic selection studies in Fars native cattle. However, this marker density will
not be able to get enough accuracy in Genome Wide Association Studies (GWAS).
Conclusion:
Results from this study can be appl
ied to determine the optimum marker density
required to achieve enough accuracy in the possible genomic studies on the Fars native cattle. Due to
recent intense inbreeding and considerable reduction in effective population size of Fars native cattle
popula
tion, the high r
2
values found in this study were as expected.
