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A 17-bp InDel (rs668420586) within goat CHCHD7 gene located in growth-related QTL affecting body measurement traits

3 Biotech volume 10, Article number: 441 (2020) Cite this article

Abstract

The Coiled-Coil-Helix-Coiled-Coil-Helix Domain Containing 7 (CHCHD7) gene was located in a growth-related major QTL that participated in the process of bone cells metabolism in animals by regulating mitochondrial copper homeostasis and cytochrome C oxidase assembly. Therefore, we speculated that CHCHD7 gene might be involved in animal growth and body size. Herein, we discovered a 17-bp insertion/deletion (indel) within the goat CHCHD7 gene. Then, we detected this variation in Shaanbei White Cashmere (SBWC, n = 1055) goats and Inner Mongolia White Cashmere (IMWC, n = 743) goats (Alathai type) using the mathematical expectation (ME) method. We then analyzed the correlation between these genotypes and goat body measurement traits. The results showed that the minor allelic frequency (MAF) was 0.011 in SBWC, and 0.048 in IMWC. In SBWC and IMWC, the reaction time by ME method was reduced by 36.78% and 27.59%, respectively, compared to the traditional method of screening samples one by one. Moreover, in SBWC goats, the 17-bp indel was significantly associated with body measurement traits (e.g. body height, and body length) in adults. In IMWC goats, the 17-bp indel was correlated with body measurement traits (e.g. body height) in weaners. In SBWC and IMWC goat populations, the body measurement traits of the individuals homozygous for 17-bp indel were higher than those in heterozygous individuals, except for the case of cannon circumference in IMWC weaners. These findings showed that the 17-bp insertion mutation within the goat CHCHD7 gene significantly affected body morphometric traits, and could provide a basis for marker-assisted selection (MAS) breeding of cashmere goats.

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Abbreviations

BH:

Body height

BL:

Body length

bp:

Base pair

BW:

Body weight

CC:

Cannon circumference

CcO:

Cytochrome C oxidase

CD:

Chest depth

CHCHD7 :

Coiled-coil-helix-coiled-coil-helix domain containing 7

Cu:

Copper

CW:

Chest width

COX23 :

Cytochrome C oxidase assembly homolog

ERR :

Estrogen-related receptor

ESRR :

Estrogen-related receptors

HG:

Heart girth

HHC:

Height at hip cross

HW:

Hip width

HWE:

Hardy–Weinberg equilibrium

IMWC:

Inner Mongolia white cashmere

InDel:

Insertion/deletion

MAF:

Minor allele frequency

MAS:

Marker-assisted selection

ME:

Mathematical expectation

NGn:

The optimal number of individuals in one mixed group

NRn:

Number of individuals in one reaction time

PCR:

Polymerase chain reaction

PIC:

Polymorphism information content

PLAG1 :

Pleiomorphic adenoma gene 1

pMAF:

Predicting minor allelic frequencies

pRR:

Predicting reduction rate

pRTn:

Predicting reaction times by the formulate

QTL :

Quantitative trait locus

RR:

Reduction rate

RTn:

Reaction times

SBWC:

Shaanbei White Cashmere

SF1 :

Steroidogenic factor 1

SF1F :

Vertebrate steroidogenic factor

SORY :

SOX/SRY-sex/testis determining and HMG box factors

SOX1 :

SRY (sex determining region Y)-box 1

SOX14 :

SRY (sex determining region Y)-box 14

SPSS:

Statistical product and service solutions

SNP:

Single nucleotide polymorphisms

TD-PCR:

Touch-down polymerase chain reaction

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Acknowledgements

This work was funded by the Provincial Key Projects of Shaanxi (2014KTDZ02-01). We were very grateful to the Qu Lei’s team membership in Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University and Life Science Research Center, Yulin University, for the samples collection of SBWC goats. We sincerely thank Ph.D. ZWX, in the College of Animal Science and Technology, Northwest A&F University, for providing experimental instruments and equipment. We greatly thank the staffs of SBWC and IMWC breeding farm, Shaanxi province, P.R. China for their collecting samples.

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Affiliations

  1. College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Haixia Li, Xinyu Wang, Hong Chen & Xianyong Lan

  2. Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, 719000, Shaanxi, People’s Republic of China

    Lei Qu

  3. Life Science Research Center, Yulin University, Yulin, 719000, Shaanxi, People’s Republic of China

    Lei Qu

Authors
  1. Haixia Li
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  2. Xinyu Wang
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  3. Hong Chen
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  4. Lei Qu
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  5. Xianyong Lan
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Contributions

HL, XL, and LQ designed the study as well as wrote the paper. HL and XW performed the experiments. HL did the statistical analysis. LQ and HC collected the samples. XL and LQ edited and reviewed the paper.

Corresponding authors

Correspondence to Haixia Li or Xianyong Lan.

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We confirm that this manuscript has not been published in whole or in part and is not being considered for publication elsewhere. There are no any ethical conflicts of interest for any of the authors.

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Li, H., Wang, X., Chen, H. et al. A 17-bp InDel (rs668420586) within goat CHCHD7 gene located in growth-related QTL affecting body measurement traits. 3 Biotech 10, 441 (2020). https://doi.org/10.1007/s13205-020-02434-8

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  • DOI: https://doi.org/10.1007/s13205-020-02434-8

Keywords

  • Goat
  • CHCHD7
  • Insertion/deletion (indel)
  • Mathematical expectation (ME)
  • Body measurement traits