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Journal of Integrative Agriculture
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Epigenome-wide DNA methylation analysis reveals differentially methylation patterns in skeletal muscle between Chinese Chenghua and Qingyu pigs
WANG Kai, WU Ping-xian, WANG Shu-jie, JI Xiang, CHEN Dong, JIANG An-an, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing
2022, 21 (
6
): 1731-1739. DOI:
10.1016/S2095-3119(21)63814-5
Abstract
(
271
)
PDF in ScienceDirect
Chenghua (CH) pig and Qingyu (QY) pig are typical Chinese native fatty breeds. CH pig is mainly distributed in Chengdu Plain, while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin. There are significant differences in their phenotypic traits, including body image, growth performance, and meat quality. This study compared several meat quality traits of CH and QY pigs and conducted a genome-wide DNA methylation analysis using reduced representation bisulfite sequencing (RRBS). It was observed that the pH at 45 min (pH
45min
,
P
=5.22e–13), lightness at 45 min (L*
45min
,
P
=4.85e–5), and lightness at 24 h (L*
24h
,
P
=3.57e–5) of CH pigs were higher than those of QY pigs. We detected 10 699 differentially methylated cytosines (DMCs) and 2 760 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in the AMPK signaling pathway, Type II diabetes mellitus, Insulin signaling pathway, mTOR signaling pathway, and Insulin resistance. Furthermore, 15 DMGs were associated with fat metabolism (
ACACA
,
CAB39
,
CRADD
,
CRTC2
,
FASN
, and
GCK
), muscle development (
HK2
,
IKBKB
,
MTOR
,
PIK3CD
,
PPARGC1A
, and
RPTOR
), or meat quality traits (
PCK1
,
PRKAG2
, and
SLC2A4
). The findings may help to understand further the epigenetic regulation mechanisms of meat quality traits in pigs and provide new basic data for the study of local pigs.
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Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing
WU Ping-xian, ZHOU Jie, WANG Kai, CHEN De-juan, YANG Xi-di, LIU Yi-hui, JIANG An-an, SHEN Lin-yuan, JIN Long, XIAO Wei-hang, JIANG Yan-zhi, LI Ming-zhou, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Xue-wei, TANG Guo-qing
2021, 20 (
9
): 2483-2490. DOI:
10.1016/S2095-3119(20)63474-8
Abstract
(
130
)
PDF in ScienceDirect
Birth weight (BW) and days to 100 kg (D100) are important economic traits that are both affected by polygenes. However, the genetic architecture of these quantitative traits is still elusive. Genotyping-by-sequencing (GBS) data containing a large number of single nucleotide polymorphisms (SNPs) have become a powerful tool in genomic analysis. To better understand their complex genetic structure, a total of 600 Yorkshire pigs were sequenced using GBS technology. After quality control, 279 787 SNPs were generated for subsequent genome-wide association study (GWAS). A total of 30 genome-wide SNPs (
P
<1.79E–07) were identified for D100. Furthermore, a total of 22 and 2 suggestive SNPs (
P
<3.57E–06) were detected for D100 and BW, respectively. Of these, one locus located on SSC12 (position: 46 226 512 bp) were evaluated to affect both BW and D100 in Yorkshire pigs, indicating the pleiotropism in different traits. Considering the function of candidate genes, two genes,
NSRP1
and
DOCK7
, were suggested as the most promising candidate genes involved in growth traits. Thus, use of GBS is able to identify novel variants and potential candidate genes for BW and D100, and provide an opportunity for improving pig growth traits using genomic selection in pigs.
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Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs
WANG Kai, WU Ping-xian, CHEN De-juan, ZHOU Jie, YANG Xi-di, JIANG An-an, MA Ji-deng, TANG Qian-zi, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing
2021, 20 (
7
): 1898-1906. DOI:
10.1016/S2095-3119(20)63488-8
Abstract
(
161
)
PDF in ScienceDirect
We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs. Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST (Z(FST)) method, and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity (ZHp) method. The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism, disease resistance, cellular processes, and biochemical signals, and several were related to body morphology and organs. They included
PPP3CA
, which plays an essential role in the transduction of intracellular Ca
2+
-mediated signals, and
WWTR1
, which plays a pivotal role in organ size control and tumor suppression. These results suggest that genes associated with body morphology were subject to selection pressure during domestication, whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding. Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.
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Detection and characterization of an isolate of
Tomato mottle mosaic virus
infecting tomato in China
ZHAN Bin-hui, CAO Ning, WANG Kai-na, ZHOU Xue-ping
2018, 17 (
05
): 1207-1212. DOI:
10.1016/S2095-3119(17)61895-1
Abstract
(
500
)
PDF in ScienceDirect
Tomato (
Solanum lycopersicum
) plants exhibiting severe leaf distortion, mottle and systemic crinkling symptoms were identified in Hainan province in China in 2016. To survey and control the disease, it is necessary to identify and characterize the pathogen causing the disease. Dot enzyme-linked immunosorbent assay showed that the crude saps of the infected tomato samples reacted positively with the monoclonal antibody against Tobacco mosaic
virus
which indicated that one or more tobamoviruses are likely associated with the disease. RT-PCR and DNA sequence analysis results further elucidated that
Tomato mottle mosaic virus
(ToMMV) in
Tobamovirus
was the pathogen causing the mottle disease in tomato. We amplified and sequenced the full-length sequence of the genome which showed the highest nucleotide identity with ToMMV YYMLJ and ToMMV TiLhaLJ isolates. The putative virus isolate was named ToMMV Hainan. Biological indexing studies showed that ToMMV Hainan can infect
Nicotiana benthamiana
,
Capsicum annuum
and
Solanum lycopersicum
showing serious symptoms. This was the first identification and characterization of ToMMV infecting tomato in Hainan of China.
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Biomass Components and Environmental Controls in Ningxia Grasslands
WANG Kai-bo, LI Jian-ping , SHANGGUAN Zhou-ping
2012, 12 (
12
): 2079-2087. DOI:
10.1016/S1671-2927(00)8746
Abstract
(
1099
)
PDF in ScienceDirect
Grassland plays an important role in the global carbon cycle and climate regulation. However, there are still large uncertainties in grassland carbon pool and also its role in global carbon cycle due to the lack of measured grassland biomass at regional scale or global scale with a unified survey method, particular for below-ground biomass. The present study, based on a total of 44 grassland sampling plots with 220 quadrats across Ningxia, investigated the characteristics of above-ground biomass (AGB), below-ground biomass (BGB), litter biomass (LB), total biomass (TB) and root:shoot ratios (R:S) for six predominantly grassland types, and their relationships with climatic factors. AGB, BGB, LB and TB varied markedly across different grassland types, the median value ranging from 28.2-692.6 g m-2 forAGB, 130.4-2036.6 g m-2 for BGB, 9.2-82.3 g m-2 for LB, and 168.0-2 681.3 g m-2 for TB. R:S showed less variation with median values from 3.2 to 5.3 (excluding marshy meadow). The different grassland types showed similar patterns of biomass allocation, with more than 70% BGB for all types. There is evidence of strong positive effects associated with mean annual precipitation (MAP) and negative effects associated with mean annual temperature (MAT) on AGB, BGB, and LB, although both factors have the opposite effect on R:S.
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Effects of Long-Term Fertilization on the Distribution of Carbon, Nitrogen and Phosphorus in Water-Stable Aggregates in Paddy Soil
WANG Wei, CHEN Wei-cai, WANG Kai-rong, XIE Xiao-li, YIN Chun-mei , CHEN An-lei
2011, 10 (
12
): 1932-1940. DOI:
10.1016/S1671-2927(11)60194-6
Abstract
(
1901
)
PDF in ScienceDirect
We investigated the size distribution of water-stable aggregates and the soil carbon, nitrogen and phosphorus concentration
over aggregate size fractions based on a long-term (1990-2006) fertilization experiment in a reddish paddy soil. The results
showed that the largest water-stable aggregate (WSA) (>5 mm) and the smallest WSA (<0.25 mm) took up the first largest
proportion (38.3%) and the second largest proportion (23.3%), respectively. Application of organic materials increased
the proportion of the large WSA (>2 mm) and decreased the proportion of the small WSA (<1 mm), resulting in an increase
in the mean weight diameter of WSA, whereas application of chemical fertilizer had little effect. Application of organic
materials, especially combined with chemical fertilizers, increased total carbon, nitrogen and phosphorus concentrations
in all sizes of WSA, and total carbon, nitrogen and phosphorus were prone to concentrate in the large WSA. Further more,
application of organic materials improved the supply effectiveness of available phosphorus, whereas had little influence
on the labile carbon in WSA. Application of chemical fertilizers improved concentrations of total and available phosphorus
in all sizes of WSA, whereas had little influence on total carbon and nitrogen contents. Economical fertilization model
maintained the soil fertility when compared with full dose of chemical fertilizers, indicating that using organic materials
could reduce chemical fertilizers by about one third.We investigated the size distribution of water-stable aggregates and the soil carbon, nitrogen and phosphorus concentration over aggregate size fractions based on a long-term (1990-2006) fertilization experiment in a reddish paddy soil. The results showed that the largest water-stable aggregate (WSA) (>5 mm) and the smallest WSA (<0.25 mm) took up the first largest proportion (38.3%) and the second largest proportion (23.3%), respectively. Application of organic materials increased the proportion of the large WSA (>2 mm) and decreased the proportion of the small WSA (<1 mm), resulting in an increase in the mean weight diameter of WSA, whereas application of chemical fertilizer had little effect. Application of organic materials, especially combined with chemical fertilizers, increased total carbon, nitrogen and phosphorus concentrations in all sizes of WSA, and total carbon, nitrogen and phosphorus were prone to concentrate in the large WSA. Further more, application of organic materials improved the supply effectiveness of available phosphorus, whereas had little influence on the labile carbon in WSA. Application of chemical fertilizers improved concentrations of total and available phosphorus in all sizes of WSA, whereas had little influence on total carbon and nitrogen contents. Economical fertilization model maintained the soil fertility when compared with full dose of chemical fertilizers, indicating that using organic materials could reduce chemical fertilizers by about one third.
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