Many different chicken breeds are found around the world, their features vary among them, and they are valuable resources.  Currently, there is a huge lack of knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these breeds of chickens.  Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved chicken breeds.  The whole-genomes of 140 chickens from 7 Shandong native breeds and 20 introduced recessive white chickens from China were re-sequenced.  Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed geographically based clusters among the chickens.  Through genome-wide scans for selective sweeps, we identified thyroid stimulating hormone receptor (TSHR, reproductive traits, circadian rhythm), erythrocyte membrane protein band 4.1 like 1 (EPB41L1, body size), and alkylglycerol monooxygenase (AGMO, aggressive behavior), as major candidate breed-specific determining genes in chickens.  In addition, we used a machine learning classification model to predict chicken breeds based on the SNPs significantly associated with recourse characteristics, and the prediction accuracy was 92%, which can effectively achieve the breed identification of Laiwu Black chickens.  We provide the first comprehensive genomic data of the Shandong indigenous chickens.  Our analyses revealed phylogeographic patterns among the Shandong indigenous chickens and candidate genes that potentially contribute to breed-specific traits of the chickens.  In addition, we developed a machine learning-based prediction model using SNP data to identify chicken breeds.  The genetic basis of indigenous chicken breeds revealed in this study is useful to better understand the mechanisms underlying the resource characteristics of chicken.

Agricultural sustainability has benefited from the broad adoption of conservation agriculture (CA) practices for decades, in which the reduction of mechanical disturbances to soil (also known as reduced tillage, RT) is one of the most essential principles for CA implementation.  Many studies have recommended the advantages of CA practices in the promotion of biodiversity, but the integrated impacts on crop productivity and biodiversity remain unclear.  Since CA has been applied in rice production in the subtropical area of southern China for several years, the effects of CA, particularly the RT methods, need to be evaluated for the local and long-term adoption.  In this study, we established an integrated network to illustrate how the reduction of tillage intensity influenced organisms including invertebrates (such as rice pests and their predators), pathogens and weeds, and then led to an impact on rice yield.  The two-year study demonstrated that major rice pests, such as rice planthoppers, stem borers and apple snails, were effectively controlled by RT practice.  Similarly, the occurrence of common diseases declined with less tillage.  Compared to the conventional tillage (CT) treatment, the density of weeds in paddy fields deceased significantly in the RT treatment.  In addition, the diversity and richness of pest predators increased remarkably in paddy fields where either reduced or no tillage was applied, which highlighted the significance of a CA strategy for the promotion of biodiversity in the agroecosystem.  More importantly, the rice yield gradually increased after the two-year reduction of tillage.  Taken together, our results suggest that the reduction of tillage intensity is beneficial for the protection of rice crops from various pests, and facilitates the sustainability of the agroecosystem and rice yield, which provides a solid basis and novel insights for the establishment of sustainable agroecosystems by CA-related practices in rice production in southern China.

Lipoxygenases (LOXs) are a group of non-heme, iron-containing enzymes and extensively involved in plant growth and development, ripening and senescence, stress responses, biosynthesis of regulatory molecules and defense reaction. In our previous study, 18 LOXs in melon genome were screened and identified, and five 13-LOX genes (CmLOX08, CmLOX10, CmLOX12, CmLOX13 and CmLOX18) were predicted to locate in chloroplast. Phylogenetic analysis result showed that the five genes have high homology with jasmonic acid (JA) biosynthesis-related LOXs from other plants. In addition, promoter analysis revealed that motifs of the five genes participate in gene expression regulated by hormones and stresses. Therefore, we analyzed the expressions of the five genes and LOX activity in leaves of four-leaf stage seedlings of oriental melon cultivar Yumeiren under abiotic stress: wounding, cold, high temperature and hydrogen peroxide (H2O2), and signal molecule treatments: methyl jasmonate (MeJA), abscisic acid (ABA) and salicylic acid (SA). Real time qPCR revealed that wounding and H2O2 induced the expressions of all the five genes. Only CmLOX08 was induced by cold while only CmLOX13 was suppressed by high temperature. ABA induced the expressions of CmLOX10 and CmLOX12 while inhibited CmLOX13 and CmLOX18. MeJA increased the 3 genes expressions except CmLOX08 and CmLOX13, whereas SA decreased the effect, apart from CmLOX12. All the abiotic stresses and signal molecules treatments increased the LOX activity in leaves of oriental melon. In summary, the results suggest that the five genes have diverse functions in abiotic stress and hormone responses, and might participate in defense response. The data generated in this study will be helpful in subcellular localization and transgenic experiment to understand their precise roles in plant defense response.

  The safety of feeding transgenic cry1Ab/cry1Ac rice (a genetically modified (GM) rice variety) to broilers was examined from an immunological perspective. Hatchling Arbor Acres chickens (240) were assigned to two dietary treatments (diets containing GM or non-GM rice) with 12 replicates per group and 10 birds per replicate. Traits were measured on one randomly selected bird from each replicate at d 21 and 42. The 42-d feeding trial revealed that cry1Ab/cry1Ac rice had no significant effect relative to non-GM rice on body weight and the immune organ indices. No significant pathological lesion in the spleen and bursa of Fabricius was found in the GM rice group. There were no significant differences in serum concentrations of immunoglobulin Y (IgY), IgM, interleukin 4 (IL-4) and IL-6 between the two groups at d 21 or 42, except for IL-6 being higher (P<0.05) in the GM-fed chickens at d 42. There were no differences in the T and B lymphocyte transformation rate and CD4+/CD8+ ratio between the two groups at d 42. Additionally, there was no significant difference between the two diets in expression of relevant genes viz. the major histocompatibility complex class II beta chain (BLB2), interferon beta 1 (IFNβ), tumour necrosis factor alpha-like (TNFα) and toll-like receptor 4 (TLR4) in the spleen and bursa of Fabricius. All the data demonstrated that transgenic cry1Ab/cry1Ac rice had no adverse effect on these aspects of immune function of broilers during 42-d feeding trial. Transgenic rice was therefore indistinguishable from non-GM rice in terms of short-term feeding in chickens.  

Potato late blight, caused by the oomycete pathogen Phytophthora infestans, is the most serious disease of potato worldwide. The adoption of varieties with resistance genes, especially broad-spectrum resistance genes, is the most efficient approach to control late blight. Solanum demissum is a well-known wild potato species from which 11 race-specific resistance genes have been identified, however, no broad-spectrum resistance genes like RB have been reported in this species. Here, we report a novel reisistance locus from S. demissum that potentially confer broad-spectrum resistance to late blight. A small segregating population of S. demissum were assessed for resistance to aggressive P. infestans isolates (race 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11). This coupled with nucleotide binding site (NBS) profiling analyses, led to the identification of three fragments that linked to the potential candidate resistance gene(s). Cloning and sequence analysis of these fragments suggested that the identified resistance gene locus is located in the region containing R2 resistance gene at chromosome 4. Based on the sequences of the cloned fragments, a co-segregating sequence characterized amplified region (SCAR) marker, RDSP, was developed. The newly identified marker RDSP will be useful for marker assisted breeding and further cloning of this potential resistance gene locus.

A comparative slaughter trial and a metabolism trial were conducted to determine the requirement of net energy (NE) and metabolizable energy (ME) by the crossbreed of German Mutton Merino×Inner Mongolia Merino for fattening from 35 to 50 kg of body weight (BW). 49 crossbred female lambs ((33.9±2.3) (SD) kg BW) of German Mutton Merino×Inner Mongolia Merino were used. 34 lambs were randomly chosen for comparative slaughter, which were offered an identical mixture diet (concentrate:roughage=55:45) at 100, 75 or 55% of ad libitum intake, whereas the remainders were used in the metabolism trial to evaluate the ME of the diet after methane production was measured by open-circuit respirometry. As feed intake decreased from 100 to 75 and 55% of ad libitum intake, the apparent digestibility of dry matter (DM) linearly increased (P=0.010) from 60.8 to 63.6 and 66.9%, respectively, and methane production decreased from 52.1 to 44.3 and 39.9 L d-1, respectively, but the ratio of methane energy to gross energy intake increased linearly (P=0.010) from 8.20 to 8.96 and 10.97%, respectively. Consequently, the ME values of the diet increased from 9.35 to 9.64 and 9.85 MJ kg-1 DM, respectively. The NE requirement for maintenance (NEm) was 255 kJ kg-1 BW0.75, and the ME requirement for maintenance (MEm) was 352 kJ kg-1 BW0.75, with a partial energy efficiency for maintenance (km) of 0.72. The NE requirement for growth (NEg) ranged from 1.26 to 4.66 MJ d-1 as average daily gains increased from 100 to 300 g d-1, with a partial energy efficiency for growth (kg) of 0.45. These results indicated that the NEg required by crossbred female lambs of German Mutton Merino×Inner Mongolia Merino was lower than the recommendation of the American or British nutritional system.

In previous experiment, we isolated a compound dibutyl phthalate (DBP) from Vaccaria segetalis which had galactopoieticfunction on mammary gland epithelial cells of dairy cow (DCMECs). In this experiment, we ascertained the metabolicregulation function of DBP on DCMECs. Many genes related to lactation including Stat5, AMPK, â-casein, Glut1, SREBP-1,PEPCK, and ACC were detected by real-time PCR. Furthermore, Stat5 and AMPK were detected by Western blot andimmunofluorescence co-localization, respectively. The results showed that DBP stimulates the expression of Stat5 andp-Stat5, thus activates Stat5 cell signal transduction pathway and stimulates â-casein synthesis. DBP also raises theactivities of Glut1 and AMPK to stimulate glucose uptake and glycometabolism and activates the expression of AMPKdownstream target genes PEPCK and ACC and expression of SREBP-1 to stimulate milk fat synthesis. In addition, theactivities of HK, G-6-PDH, ICDH, ATPase, and energy charges were stimulated by DBP to increase the energy metabolismlevel of DCMECs. The results showed DBP stimulates energy metabolism related to galactopoietic function in DCMECs.