Whole-genome bisulfite sequencing of abdominal adipose reveals DNA methylation pattern variations in broiler lines divergently selected for fatness

The methylation status of pivotal genes involved in fat deposition in chickens has been extensively studied. However, the whole-genome DNA methylation profiles of broiler abdominal adipose tissue remain poorly understood. Using whole-genome bisulfite sequencing, we generated DNA methylation profiles of chicken abdominal adipose tissue from Northeast Agricultural University broiler lines divergently selected for abdominal fat content. We aimed to explore whether DNA methylation was associated with abdominal fat deposition in broilers. The whole-genome DNA methylation profiles of fat- and lean-line broilers abdominal adipose tissue were constructed. The DNA methylation levels of functional genomic regions in the fat broiler were higher than those in the lean broiler, especially in the 3′ untranslated regions (UTRs) and exons in the non-CG contexts. Additionally, we identified 29,631 differentially methylated regions and, subsequently, annotated 6,484 and 2,016 differentially methylated genes (DMGs) in the gene body and promoter regions between the two lines, respectively. Functional annotation showed that the DMGs in promoter regions were significantly enriched mainly in the triglyceride catabolic process, lipid metabolism-related pathways, and extracellular matrix signal pathways. When the DMG in promoter regions and differentially expressed genes were integrated, we identified 30 genes with DNA methylation levels that negatively correlated with their messenger RNA (mRNA) expression, of which CMSS1 reached significant levels (false discovery rate < 0.05). These 30 genes were mainly involved in fatty acid metabolism, peroxisome-proliferator-activated receptor signaling, Wnt signaling pathways, transmembrane transport, RNA degradation, and glycosaminoglycan degradation. Comparing the DNA methylation profiles between fat- and lean-line broilers demonstrated that DNA methylation is involved in regulating broiler abdominal fat deposition. Our study offers a basis for further exploring the underlying mechanisms of abdominal adipose deposition in broilers.     

Whole-genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

The primary objective of most horse breeding operations was to maximize reproductive efficiency and minimize the cost of producing live foals. Here, we compared individual horses from the Thoroughbred population (n = 17), known as a horse breed with poor reproductive performance, with other six horse populations (n = 28), to detect genomic signatures of positive selection underlying of reproductive traits. A number of protein-coding genes with significant (p-value <.01) higher F_ST values (616 genes) and a lower value for nucleotide diversity (π) (310 genes) were identified. The results of our study revealed some candidate genes such as IGFBP2, IGFBP5, GDF9, BRINP3 and GRID1 are possibly associated with functions influencing reproductive traits. These genes may have been under selection due to their essential roles in reproduction performance in horses. The candidate selected genes identified in this work should be of great interest for future research into genetic architecture of traits relevant to horse breeding programmes.     

Genetic diversity and thermotolerance in Holstein cows: Pathway analysis and marker development using whole-genome sequencing

Heat stress causes extensive losses in the dairy sector, due to negative effects on milk production and reproduction. Cows have evolved a series of protective mechanisms, (physiological, biochemical, behavioural) to cope with the thermostressing environments, which have allowed the preservation of productive and reproductive potential of specific animals during summer; these animals are considered thermotolerant and could be used to design programs of selective breeding. These programs, targeting the generations of a population of heat-resistant animals, would increase the frequency of the desired phenotypes, tackling the financial losses on one hand and reducing the carbon footprints of the dairy sector on the other. The development of genomics techniques has enabled genome wide variant calling, to detect SNPs associated with the desired phenotypes. In this study, we used a comparative genomics approach to detect genetic variation associated with thermotolerance and to design molecular markers for characterizing the animals as tolerant/sensitive. A total of 40 cows from each group were split in four sequencing pools and a whole-genome sequencing approach was used. Results and conclusion: Genome-wide genetic variation between groups was characterized and enrichment analysis revealed specific pathways which participate in the adaptive mechanisms of thermotolerance, implicated into systemic and cellular responses, including the immune system functionality, Heat Stress and Unfolded Protein Response. The markers made a promising set of results, as specific SNPs in five genes encoding for Heat Shock Proteins were significantly associated with thermotolerance.     

Analysis of genetic and cultural conservation value of three indigenous Croatian cattle breeds in a local and global context

It is widely accepted that autochthonous cattle breeds can be important genetic resources for unforeseeable environmental conditions in the future. Apart from that, they often represent local culture and tradition and thus assist in the awareness of ethnic identity of a country. In Croatia, there are only three indigenous cattle breeds, Croatian Bu?a, Slavonian Syrmian Podolian and Istrian Cattle. All of them are threatened but specialized in a particular habitat and production system. We analysed 93 microsatellites in 51 animals of each breed to get thorough information about genetic diversity and population structure. We further set them within an existing frame of additional 16 breeds that have been genotyped for the same marker set and cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the north‐west of Europe. The cultural value was evaluated regarding the role in landscape, gastronomy, folklore and handicraft. The overall results recognize Croatian Bu?a being partly admixed but harbouring an enormous genetic diversity comparable with other traditional unselected Bu?a breeds in the Anatolian and Balkan areas. The Podolian cattle showed the lowest genetic diversity at the highest genetic distance to all remaining breeds but are playing an important role as part of the cultural landscape and thus contribute to the tourist industry. The genetic diversity of the Istrian cattle was found in the middle range of this study. It is already included in the tourist industry as a local food speciality. Current and future conservation strategies are discussed.     

奶牛养殖场环境微生物群落结构及多样性研究

为了研究奶牛养殖场部分环境因素与奶牛乳房处的细菌多样性和差异性,将分别取自牛乳房擦拭样品(C1)、榨乳设备(E)、粪便(F)、冲洗和养殖饮用水(W)、生乳运输罐(E2) 5种样本的6个生物学重复共计30个样品使用基于16SrRNA (V3～V4区)的高通量测序技术,并采用生物信息学的方法分析了不同来源样本的细菌群落结构...     

Genetic diversity in Trypanosoma theileri from Sri Lankan cattle and water buffaloes

Trypanosoma theileri is a hemoprotozoan parasite that infects various ruminant species. We investigated the epidemiology of this parasite among cattle and water buffalo populations bred in Sri Lanka, using a diagnostic PCR assay based on the cathepsin L-like protein (CATL) gene. Blood DNA samples sourced from cattle (n = 316) and water buffaloes (n = 320) bred in different geographical areas of Sri Lanka were PCR screened for T. theileri. Parasite DNA was detected in cattle and water buffaloes alike in all the sampling locations. The overall T. theileri-positive rate was higher in water buffaloes (15.9%) than in cattle (7.6%). Subsequently, PCR amplicons were sequenced and the partial CATL sequences were phylogenetically analyzed. The identity values for the CATL gene were 89.6–99.7% among the cattle-derived sequences, compared with values of 90.7–100% for the buffalo-derived sequences. However, the cattle-derived sequences shared 88.2–100% identity values with those from buffaloes. In the phylogenetic tree, the Sri Lankan CATL gene sequences fell into two major clades (TthI and TthII), both of which contain CATL sequences from several other countries. Although most of the CATL sequences from Sri Lankan cattle and buffaloes clustered independently, two buffalo-derived sequences were observed to be closely related to those of the Sri Lankan cattle. Furthermore, a Sri Lankan buffalo sequence clustered with CATL gene sequences from Brazilian buffalo and Thai cattle. In addition to reporting the first PCR-based survey of T. theileri among Sri Lankan-bred cattle and water buffaloes, the present study found that some of the CATL gene fragments sourced from water buffaloes shared similarity with those determined from cattle in this country.     

Prevalence,quantitative load and genetic diversity of Campylobacter spp. in dairy cattle herds in Lithuania

Background

Campylobacteriosis is a zoonotic disease, and animals such as poultry, pigs and cattle may act as reservoirs for Campylobacter spp. Cattle shed Campylobacter spp. into the environment and they can act as a reservoir for human infection directly via contact with cattle or their faeces or indirectly by consumption of contaminated food. The aim of this study was to determine the prevalence, the quantitative load and the genetic strain diversity of Campylobacter spp. in dairy cattle of different age groups.

Results

Faecal samples of 200 dairy cattle from three farms in the central part of Lithuania were collected and examined for Campylobacter. Cattle herds of all three farms were Campylobacter spp. positive, with a prevalence ranging from 75% (farm I), 77.5% (farm II) to 83.3% (farm III). Overall, the highest prevalence was detected in calves (86.5%) and heifers (86.2%). In contrast, the lowest Campylobacter prevalence was detectable in dairy cows (60.6%). C. jejuni, C. coli, C. lari and C. fetus subsp. fetus were identified in faecal samples of dairy cattle. C. upsaliensis was not detectable in any sample. The high counts of Campylobacter spp. were observed in faecal material of dairy cattle (average 4.5 log₁₀ cfu/g). The highest numbers of Campylobacter spp. were found in faecal samples from calves (average 5.3 log₁₀ cfu/g), whereas, faecal samples from cows harboured the lowest number of Campylobacter spp. (average 3.7 log₁₀ cfu/g). Genotyping by flaA PCR-RFLP analysis of selected C. jejuni isolates showed that some genotypes were present in all farms and all age groups. However, farm or age specific genotypes were also identified.

Conclusions

Future studies are needed to investigate risk factors related to the degree of colonisation in cattle. Based on that, possible measures to reduce the colonisation and subsequent shedding of Campylobacter in cattle could be established. It is important to further investigate the epidemiology of Campylobacter in the cattle population in order to assess associated risks to public health.     

Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis

The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (N_ge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N_ge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.     

甘肃地方绵羊品种微卫星遗传多样性与系统发育分析

通过对甘肃省6个地方绵羊品种(240只个体)15个微卫星座位的等位基因的研究,结果共发现了179个等位基因。其中在藏羊中发现的等位基因数最多(136个),兰州大尾羊最少(94个)。多态信息含量、期望杂合度和观察杂合度的数据表明:在研究的6个绵羊品种中藏羊和甘肃高山细毛羊的遗传多样性较丰富,而兰州大尾羊和岷县黑裘皮羊的遗传多样性较低。DA遗传距离和D s遗传距离构建的NJ系统发育树均表明:兰州大尾羊、蒙古羊和滩羊具有较近的亲缘关系,预示这3个品种可能具有相同的原始祖先。而甘肃高山细毛羊与其他5个甘肃地方品种的遗传距离较远,另为一类。     

河北省森林草原区草本植物物种多样性和功能多样性

理解物种多样性和功能多样性之间的关系以及分析它们对环境变化的响应,有利于揭示生物多样性的影响因素。本研究以塞罕坝地区不同植被类型(草地、灌木林和天然次生林)的草本群落为研究对象,分析了物种多样性(物种丰富度、Shannon-Wiener多样性和Pielou均匀度)和功能多样性测度指标(功能丰富度、功能均匀度和功能离散度)之间的相互关系,并采用相似性分析检验(ANOSIM)和冗余度(RDA)分析等方法研究了它们随植被类型和环境因子的变化规律。结果表明,草地中草本植物物种丰富度、Shannon-Wiener多样性指数显著高于灌木林和天然次生林中的草本群落(P<0.05),而功能丰富度指数在草地中最低(P<0.05),功能均匀度和功能离散度在灌木林中最低(P<0.05),Pielou均匀度指数在不同植被类型间差异不显著(P>0.05);功能丰富度与物种丰富度、Shannon-Wiener多样性指数显著负相关(P<0.01),功能离散度与物种均匀度显著正相关(P<0.01),而功能均匀度与所有物种多样性指数均不相关(P>0.05);影响物种多样性的主要因子有土壤含水量、土壤有机质、土壤pH值、土壤全氮含量和坡向,影响功能多样性的主要因子有土壤有机质、土层深度、土壤含水量和海拔。物种多样性和功能多样性分布主要受土壤因子的影响,分别占到总解释变异的29.1%和29.8%。本研究结果表明研究区草本植物物种多样性和功能多样性变化相对独立,物种多样性可能主要是由资源可利用程度决定,而功能多样性可能是生态位分化即环境筛选和物种间相互作用共同决定。     

Genetic diversity and origin of Gayal and cattle in Yunnan revealed by mtDNA control region and SRY gene sequence variation

There are hump, humpless cattle and gayal distributed in Yunnan province, south‐west China, but their genetic background remains unclear. To determine the origin and genetic diversity of Yunnan gayal and cattle (Diqing, Nujiang and Wenshan cattle), we analysed mtDNA control region sequences of 71 samples and SRY gene sequences of 39 samples, together with the available sequences in GenBank. The neighbour‐joining phylogeny and the reduced median network analysis showed that Yunnan gayal originated from the hybridization between male Bos frontalis and female Bos taurus or Bos indicus, and that Yunnan cattle mostly originated from B. indicus, also containing some hybrids of male B. indicus and female B. taurus. The phylogenetic pattern of Yunnan cattle was consistent with the recently described cattle matrilineal pool from China and indicated more contribution to the Yunnan cattle from B. indicus than from B. taurus.     

Occurrence and genetic diversity of hemoplasmas in beef cattle from the Brazilian Pantanal,an endemic area for bovine trypanosomiasis in South America

Hemotropic mycoplasmas (hemoplasmas) are Gram-negative bacteria that parasitize the erythrocyte surface of a wide variety of mammals. The present study aimed at investigating the occurrence of hemoplasmas in beef cattle in the Brazilian Pantanal, an area endemic for bovine trypanosomiasis in South America. Additionally, the objective of this study was to characterize molecularly the genotypes of the found hemoplasmas. For this purpose, blood and serum samples of 400 beef cattle were collected from five properties in Corumbá, Nhecolândia sub-region, Mato Grosso do Sul, in Midwest Brazil. Blood samples underwent DNA extraction and standard 16S rRNA gene-based PCR assays for hemoplasmas. The sequences obtained were submitted to phylogenetic inferences, distance analysis, and genotype diversity. The Indirect Enzyme-Linked Immunoabsorbent Assay (iELISA) indicated the presence of anti-Trypanosoma vivax IgG antibodies in 89.75% of the animals sampled, confirming the endemicity of said agent in the studied region. Among the 400 bovine blood samples tested, 2.25% (9/400) were positive for hemoplasmas in cPCR. The phylogenetic analysis of the obtained sequences confirmed the presence of 'Candidatus Mycoplasma haemobos' and Mycoplasma wenyonii DNA in 0.5% (2/400) and 1.75% (7/400) animals, respectively. Five genotypes of M. wenyonii and one of 'Candidatus M. haemobos' were detected among the sequenced amplicons. The present study showed low molecular occurrence of haemoplasmas in beef cattle sampled in the Brazilian Pantanal, an area endemic for bovine trypanosomiasis. Despite of the conservation of the 16S rRNA gene, there was considerable diversity of hemoplasma genotypes infecting the sampled beef cattle.     

Genetic diversity and historic introgression in German Angler and Red Dual Purpose cattle and possibilities to reverse introgression

Recovering native uniqueness has major importance for breeds with historic introgression. The aim of the study was to estimate population genetic parameters for two local red cattle breeds from Northern Germany and to study possibilities to reverse introgression. Genealogical information consisted of 90,783 individuals for German Angler and 187,255 individuals for Red Dual-Purpose cattle breed, with additional information on sex, born, breed, status, and conventional breeding values. It is concluded that the native genetic contribution could be included as an additional trait in the total merit index in order to recover a part of the native genetic background. Native contributions should be estimated in the long term from marker data in order to account for Mendelian sampling. The maintenance of a sufficient genetic diversity of native alleles can be achieved by an advanced OCS with appropriate constraints.     

Isolation and sero-genomo-epidemiological studies on Brucella infection in dairy cattle in Meghalaya,India

In this study, we report the serological, bacteriological and whole genome sequencing data of a 6 years study of Brucella abortus in Meghalaya, India. Investigation of 3060 sera samples indicated overall prevalence of 6.4% by Rose Bengal Plate Test and 10.7% by ELISA. Considerably higher prevalence was observed among milk samples (17.5%, n = 362) and in blood samples (37.7%, n = 262) by direct PCR. Clinical samples (n = 94) from late abortion cases yielded 11 B. abortus isolates. Multi-locus sequence typing indicated circulation of single sequence type, ST1. Whole genome sequencing (n = 8) and phylogenomic analysis revealed close clustering of majority of isolates in two clusters alongwith genomes from other countries, indicating global relatedness among B. abortus. Taken together, the results of our study revealed the putative hotspot of infection in the dairy-dominant districts of the state and also calls for concerted One Health based action for prevention and control of this zoonotic disease.     

Analysis of genetic diversity and phylogenetic relationship of red deer subspecies in XinJiang,China

Polymorphisms for seven microsatellite loci in three red deer subspecies (9 populations) found in XinJiang were detected by polymerase chain reaction (PCR), 12% nondenaturation polyacrylamide gel electrophoresis and the Sanguinetti silver staining method. Numbers of alleles, average effective numbers of alleles (E) and the average rate of homozygosity, allelic frequencies of seven microsatellite loci, polymorphism information content (PIC), mean heterozygosity (H) and genetic distances among the populations were calculated for each population. Dendrograms were constructed based on genetic distances by the neighbor‐joining method (NJ), utilizing molecular evolutionary genetics analysis software PHYLIP (3.6). The phylogenetic tree was constructed based on allelic frequencies using maximum likelihood (ML); the bootstrap value was estimated by bootstrap test in the tree. Lastly, phylogenesis was analyzed. The results showed that four of the seven microsatellite loci were highly polymorphic, but BMS2508 and Celjp0023 showed no polymorphism and BM5004 was a neutral polymorphism. It is our conclusion that the four microsatellite loci are effective DNA markers for the analysis of genetic diversity and phylogenetic relationships among the three red deer subspecies. The mean PIC, H and E‐values across the microsatellite loci were 0.5393, 0.5736 and 2.64, which showed that these microsatellite loci are effective DNA markers for the genetic analysis of red deer. C.e. songaricus populations from Regiment 104, 151 and Hami are clustered together. C.e. yarkandensis populations from Regiment 35, Xaya and Alaer are clustered together. These two clusters also cluster together. Lastly, C.e. sibiricus populations from Burqin, Regiment 188 and the first two clusters were clustered together. The phylogenetic relationship among different red deer populations is consistent with the known origin, history of breeding and geographic distributions of populations.     

荷斯坦奶牛瘤胃微生物分离鉴定及多样性分析

研究为分离获得荷斯坦奶牛瘤胃内容物中的细菌,建立系统进化树,获取有益菌种。采用培养组学技术和16S rDNA分子鉴定方法相结合,对3头健康荷斯坦奶牛瘤胃内容物中细菌进行分离培养。共分离得到105株细菌,包括肠球菌属(Enterococcus)共15株14.29%,芽孢杆菌属(bacillus)共11株10.48%,不动杆菌属(Acinetobacter)共14株13.33%,葡萄球菌属(Staphylococcus)共22株20.95%,梭菌属(Clostridium)共1株0.95%,狭义梭菌属(Clostridium sensu stricto)共2株1.90%,短杆菌科(Brevibacteriaceae)共2株1.90%,链球菌属(Streptococcus)共11株10.48%,气球菌属(Aerococcus)共4株3.81%,柠檬酸杆菌属(Citrobacter)共14株13.33%,杆菌属(Brachybacterium)共1株0.95%,克雷伯氏菌属(Klebsiella)共1株0.95%,普罗维登斯菌属(Providencia)共3株2.86%,沙雷氏菌属(Serratia)共4株3.81%。结果中所占比例最高的菌属是葡萄球菌属;系统进化树分析和GenBank中的同源性比对结果发现,从细菌门、纲、目、科、属、种分析,分支明确;26个菌种同源性都在95.01%~100%之间。分离纯化出11株芽孢杆菌属(Bacillus)细菌具有潜在益生菌活性。可作为饲料添加剂饲喂荷斯坦奶牛。     

Cetacean occurrence and diversity in whale-watching waters off Mirissa,Southern Sri Lanka

Scientific information is vital to the conservation of cetaceans and the management of whale-watching activities. The southern coastal waters of Sri Lanka are near a narrow continental shelf and biologically abundant in cetacean species. Although the occurrence of cetaceans has been investigated in certain waters of Sri Lanka, few surveys have been conducted along the southern coast. To fill this gap, we conducted boat-based surveys from January to May 2017 to investigate the occurrence, diversity, and behavior of cetaceans in the waters off Mirissa, covering a survey area of 788.9 km². During 55 survey days, we recorded a total of 242 cetacean sightings and identified at least 9 species (3 mysticetes and 6 odontocetes). The blue whale was the most common mysticete species (167 of 174 mysticete encounters), followed by the Omura's whale (4 of 174) and Bryde's whale (3 of 174). The spinner dolphin was the most common odontocete species (28 of 68 odontocete encounters), followed by the sperm whale (18 of 68), common bottlenose dolphin (13 of 68), short-finned pilot whale (5 of 68), melon-headed whale (2 of 68), and killer whale. Blue whales and sperm whales exhibited a clear preference for outer shelf and high slope areas, and blue whales were observed feeding along these waters. The present study provides near-baseline information on cetacean occurrence and diversity in whale-watching waters off southern Sri Lanka, and highlights the urgent need for proper management strategies for whale-watching activities.     

河西走廊山地-绿洲-荒漠复合生态系统的景观多样性

采用GIS技术对河西走廊山地-绿洲、荒漠复合生态系统的景观多样性进行了研究。研究结果表明：绿洲景观生态系统和山地景观生态系统的最大景观多样性指数最大；绿洲景观生态系统的景观多样性指数最大，其次为山地景观生态系统，荒漠景观生态系统由4种景观组分组成，其最大景观多样性指数和景观多样性指数最小；均匀度最高的为绿洲景观生态系统，其次为山地景观生态系统，最低的为荒漠景观生态系统；三类景观生态系统的景观优势度都不高。     

高山嵩草草甸初级生产力、多样性与土壤因子的关系

为了揭示高寒草甸初级生产力与土壤因子及多样性指数的关系,本文选择青藏高原三江源区具有代表性的高山嵩草矮嵩草草地型、高山嵩草杂类草草地型和高山嵩草圆穗蓼草地型,进行植物多样性、生产力及土壤养分的分析研究。结果表明：不同类型高山嵩草草甸生物量、群落多样性、土壤理化性质都存在显著差异（P ＜0．05）,其中高山嵩草圆穗蓼草地生产力最高,物种数最多,土壤营养成分含量最高。相关性分析表明：地上生物量及优良牧草生物量与土壤理化性质呈显著相关（P ＜0．05）,优良牧草生物量与土壤有机质呈极显著正相关（P ＜0．01）。物种数的多寡与土壤养分呈显著相关（P ＜0．05）,而群落结构的均匀度及多样性是与植物都需要的大量元素钾呈正相关的（P ＜0．01）。优势物种的竞争能力是通过土壤的有限养分（速效磷）体现的,两者呈显著正相关（P ＜0．05）,因而地上生物量及优良牧草生物量与速效磷呈极显著正相关（P ＜0．01）。而矿物氮（包含碱解氮）对丰富度指数、初级生产力有不可替代的作用。     

Ensiling characteristics of total mixed ration prepared with local feed resources in Mozambique and their effects on nutrition value and milk production in Jersey dairy cattle

To effectively utilize total mixed ration (TMR) prepared with locally available feed resources, we studied the nutritional value and milk production in Jersey dairy cattle fed a local general diet (LGD) and fermented TMR in Mozambique. Ten head of Jersey dairy cattle with 337 ± 19.8 kg body weight, aged 3–4 years in mid location were used in this study. The LGD diet was designed following the general feeding method of local smallholding farms; it contained native grass, Napier grass, wheat bran, and mineral–vitamin mix. Fermented TMR was prepared using Napier grass, corn bran, wheat bran, formula feed, and mineral–vitamin mix. Fermented TMR was preserved as good quality, with a relatively low pH and high lactic acid content. Compared to LGD, fermented TMR significantly improved the dry matter intake and digestibility in dairy cattle. Milk yield was significantly higher in dairy cattle fed with TMR than in those fed with LGD, by 3.75 L/d; milk quality was not significantly different between treatments. The results confirmed that LGD had a low dry matter intake and milk yield, and fermented TMR prepared with local feed resources can attain good quality and improve milk yield in dairy cattle in Mozambique.