Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle

Bone weight, defined as the total weight of the bones in all the forequarter and hindquarter joints, can reflect somebody conformation traits and skeletal diseases. To gain a better understanding of the genetic determinants of bone weight, we used a composite strategy including multimarker and rare‐marker association to perform genomewide association studies (GWAS) for that character in Simmental cattle. Our strategy consisted of three models: (i) A traditional linear mixed model (LMM) was applied (Q+K‐LMM); (ii) single nucleotide polymorphisms (SNPs) with p‐values less than .05 from the LMM were selected to undergo the least absolute shrinkage and selector operator (Lasso) in the second stage (LMM‐Lasso); (iii) genes containing two or more rare SNPs were examined by performing the sequence kernel association test (gene‐based SKAT). A total of 1,225 cattle were genotyped with an Illumina BovineHD BeadChip containing 770,000 SNPs. After the quality‐control procedures, 1,217 individuals with 608,696 common SNPs and 105,787 rare SNPs (with 0.001 < minor allele frequency [MAF] <0.05) remained in the sample for analysis. A traditional LMM successfully mapped three genes associated with bone weight, while LMM‐Lasso identified nine genes, which included all genes found by traditional LMM. Only a single gene, EPHB3, surpassed the significance threshold after Bonferroni correction in gene‐based SKAT. In conclusion, based on functional annotation and results from previous endeavours, we believe that LCORL, RIMS2, LAP3, PRKAR2B, CHSY1, MAP2K6 and EPHB3 are candidate genes for bone weight. In general, such a comprehensive strategy for GWAS may be useful for researchers seeking to probe the full genetic architecture underlying economic traits in livestock.     

Intra‐abdominal cystic lymphangiomatosis in a Thoroughbred foal

Cystic lymphangiomas are rare malformations of the lymphatics that result in the formation of a cystic mass. Where multiple cysts are seen, the condition is termed cystic lymphangiomatosis. This case describes the diagnosis and unique management of cystic lymphangiomatosis in a 10‐day‐old Thoroughbred foal. Ultrasonography, histopathology and laparoscopy were essential for diagnosis and appreciation of the extent of disease. Ultimately, the cystic lymphangiomatosis was so extensive in this foal that complete surgical excision was considered impossible and the presence of adhesions within the abdomen indicated a very poor long‐term prognosis; the owners elected for euthanasia at age 14 weeks. Although rare, lymphangioma and lymphangiomatosis should be considered as a differential diagnosis for an intra‐abdominal mass in a young horse.     

Impact of cold-season grazing and supplementary feeding on rumen metabolic parameters and micro-organisms in the ewes of Gansu Alpine Fine Wool Sheep北大核心CSCD

An experiment was conducted to scientifically identify the appropriate feed for Gansu Alpine Fine Wool ewes in order to change the animals' breeding mode, which currently can only be mated at the age of 2.5 years due to insufficient nutritional supply. The experiment selected 48 12-month-old ewes and randomly divided them into group a (Diet 1), group b (Diet 2), group c (Diet 3), and a control group with no supplementary feeding. The feed test was run for 90 days. The rumen pH of groups a and b were very significantly higher (P<0.01) or group c significantly lower (P<0.05) than control group. The rumen ammonia nitrogen, protein nitrogen and total nitrogen of groups a, b and c were all higher than control group (P<0.01). The total volatile fatty acids of group a and b were all higher than the control group (P<0.01), group b significantly higher than group c (P<0.05). The molar ratio of acetic acid and propionic acid in group a was very significantly higher than control group (P<0.01), group b and c were significantly higher than control group (P<0.05). The molar ratio of butyric acid in group a was very significantly higher than group c (P<0.01). The ratio of acetic acid and propionic acid in group b was significantly lower than control group (P<0.05). The number of several rumen fiber-degrading bacteria and protozoa in groups a, b and c were very significantly (P<0.01) or significantly (P<0.05) higher than the control. In conclusion, this study shows that supplementary feeding can positively affect the rumen metabolic parameters and the number of several rumen microorganisms in Gansu Alpine Fine Wool ewes. In general, the effects of Diet 1 were the strongest, while Diet 2 also produced notable improvements. © 2018, Editorial Office of Acta Prataculturae Sinica. All rights reserved.     

Response of labile organic C and N pools to plastic film removal from semiarid farmland soil

To examine the effects of plastic film removal on grain yield and soil organic matter (SOM), a spring maize (Zea may L.) field experiment was conducted for 5 yr at Changwu Agricultural and Ecological Experimental Station of Northwest China. Compared with traditional plastic film mulching during entire growing stages (FM), plastic film removal at the silking stage (RM) resulted in a 6.3% higher average maize yield. Under the RM treatment, soil organic carbon and total nitrogen significantly increased after the 5‐yr cultivation in the 0‐ to 20‐cm layer. Significant increases in extractable organic C (EOC), KMnO₄‐oxidizable C (KMnO₄‐C) and C management index (CMI) in the 0‐ to 20‐cm layer, and light fraction organic C and EOC in the 20‐ to 40‐cm layer were observed in response to plastic film removal after the 1‐yr treatment; the responses were more significant after 5 yr. Under the RM treatment, significant increases in microbial biomass C, light fraction organic N, extractable organic N, KMnO₄‐C and CMI were also observed after five years in the 20‐ to 40‐cm layer. Moreover, KMnO₄‐C and EOC were much more sensitive than other labile SOM fractions to the application of RM, even after only 1 yr of cultivation. Therefore, compared with mulching for the whole growing season, plastic film removal at the maize silking stage is an effective option for increasing yields and enhancing SOM concentration and soil sustainability in the regions with semiarid monsoon climates that have sufficient rainfall during maize reproductive stages.     

Pedotransfer functions to assess adsorbed phosphate using iron oxide content and magnetic susceptibility in an Oxisol

Adsorbed phosphate in soils can be chemically extracted; however, this process is both time‐consuming and not cost‐effective if large numbers of samples have to be analysed. Indirect assessment of adsorbed phosphate by pedotransfer functions (PTFs) can help optimize fertilizer strategies. This study aimed to evaluate the spatial variability of adsorbed phosphate (P_ads), iron oxides and magnetic susceptibility (MS) in oxisols and to calibrate PTFs to predict P_ads. A total of 308 soil samples were collected from Hapludox and Eutrudox soils formed from sandstone in Brazil. The contents of clay (196–607 g/kg), iron oxides (40–165 g/kg), MS (1.2–29 × 10^?6 m³/kg) and P_ads (327–842 mg/kg) were in the range of typical values for these highly weathered soils. This study showed that the attributes studied were spatially dependent. Geomorphic surfaces enabled understanding of spatial variability and helped to develop a more efficient sampling scheme to calibrate PTFs. Moreover, the adsorbed phosphate in these oxisols could be predicted by a PTF using iron oxides and MS as predictors. The MS attribute enabled the most accurate prediction (concordance coefficient = 0.95, root‐mean‐square error = 46 mg/kg and relative improvement in root‐mean‐square error = ?4.12) of spatial variability through PTF compared to other predictors.     

Symbiotic N<Subscript>2</Subscript> fixation and nitrate utilisation in irrigated lucerne (<Emphasis Type="Italic">Medicago sativa</Emphasis>) systems

Symbiotic N₂ fixation by lucerne (Medicago sativa) has capacity to provide significant inputs of N to agro-ecosystems, and the species has also been shown to scavenge soil mineral N and thus act as a sink for excess reactive N. The balance between these two N cycle processes was investigated in an extensive irrigated lucerne growing region where nitrate contamination of groundwater has been reported. We sampled 18 permanent pure lucerne stands under irrigation for standing dry matter, total shoot N, and N₂ fixation using ¹⁵N natural abundance along with activity of the inducible enzyme nitrate reductase as indicators of use of soil NO₃⁻ by lucerne. On average 65% of lucerne N was obtained from symbiotic N₂ fixation. Converting standing dry matter estimates to annual N₂ fixation amounts we calculated average N₂ fixation of 311 kg N/ha, including N in roots and nodules. Uptake of N from soil by lucerne was calculated to be 181 kg N/ha/year. We were not able to identify the source of this soil mineral N, although nitrate reductase activity of lucerne was higher than that of non-N₂ fixing species examined.