DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally employed long (400–800 bp) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intra-species genetic variation. We report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterise four million SNPs and four hundred thousand structural variants, many of which are previously unknown. Our approach is effective for accurate, rapid and economical whole genome re-sequencing and many other biomedical applications.

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Fat tailed sheep breeds are known for their adaptation to nutritional stress, among other harsh production conditions. Damara sheep, native to Southern Africa, have recently been exported to other areas of the world, particularly Australia, aiming to produce lamb in semi-arid regions. Damaras have a unique hanging fat tail, a fat depot able to be mobilized under nutritional stress. In this article we perform an in-depth characterization of the fatty acid profiles of the fat tail in underfed and control Damara rams. Profiles were very similar between experimental groups, with the exception of palmitic acid (16:0) that was lower (P = 0.014) in underfed animals. However, the most striking result was the very high proportions of non-terminal branched chain fatty acids found in the fat tail adipose tissue, as well as the gastrocnemius muscle of Damara rams. The muscle of Dorper and Merino rams used in the same experiment did not present non-terminal branched chain fatty acids, suggesting that Damara rams have a unique lipid metabolism. Herein, we interpret this trait relating it to a higher ability of Damara sheep to digest fibrous fodder and to putative differences in the propionate metabolism by comparison to other sheep breeds.

Seasonal weight loss (SWL) is the most pressing constraint in ruminant production systems in tropical climates. SWL is controlled using supplementation, which is costly and difficult to implement in extensive systems, or using breeds adapted to tropical hot dry climates, like the Damara and Dorper. Albeit 15 years in Australia, little is known on how these sheep compare to Australian Merino. Here, the responses of the Damara, Dorper and Merino breeds to nutritional stress were compared. Seventy-two 6-month-old ram lambs, 24 from each breed, were allocated to growth (gaining 100 g/day) or restricted diets (losing 100 g/day, 85% of maintenance needs). Animals were weighed and carcass and meat characteristics determined. Results point out to the existence of important differences between the three genotypes, in particular between the Merino and the Southern African breeds. Additionally, Merino ram lambs seem to have been more influenced by SWL than the other two, with consequences on meat characteristics.

The nutritional status of females during pregnancy can play a critical role in the postnatal growth and development of the offspring, often leading to permanent changes ('fetal programming'). The Sertoli cells are a strong candidate for fetal programming of future performance because the number of Sertoli cells is highly correlated with adult testicular size and the maximum rate of sperm production. For Merino ewes, we imposed different levels of metabolizable energy (ME) intake (LowME: 70% of requirements for maintenance of ewe body mass and normal growth of conceptus (n = 13); HighME: 110% of those requirements (n = 12)) from Week 10 of pregnancy until parturition and then tested for effects on testicular histology in newborn males. Pregnant ewes were weighed weekly and lambs were weighed at birth and 2 days later. Blood was sampled at the same times. LowME ewes did not gain weight, whereas HighME ewes gained 17% over their pretreatment weight. Birthweights were higher in HighME lambs than in LowME lambs. Paired testes tended to be heavier in the HighME group than in the LowME group (P=0.08). The diameter of the testicular cords did not differ. The absolute volume of testicular cords (0.36 ± 0.02 v. 0.30 ± 0.02 mL for HighME v. LowME, respectively; P=0.03) and the number of Sertoli cells (43.0�±�2.5 v. 34.5 ± 2.0 × 108 for HighME v. LowME, respectively; P=0.018) per testis were both greater in the HighME than in the LowME group. Plasma follicle-stimulating hormone concentrations were not significantly affected at birth or 2 days later. We conclude that undernutrition during pregnancy can reduce testicular development in the newborn. Depending on the ability of the Sertoli cell population to recover between birth and puberty, this may limit the ultimate number of Sertoli cells and, hence, the future capacity for sperm production and fertility.

We have developed an experimental model in which groups of ewes are simultaneously experiencing the first ovarian follicular wave of their oestrous cycle. We used this 'first-wave model' in a 2!2 factorial experiment (ten ewes per group) to study the effect of body condition (BC) and a short-term supplement on follicular dynamics and ovulation rate. The 'first-wave' was established by giving ewes three injections of prostaglandin (PG), 7 days apart. The 6-day supplement (lupin grain) began 2 days after the second PG injection and continued until the third. Follicles were studied by ultrasound, and blood was sampled to measure glucose and hormones. The supplement increased (P!0.01) the concentrations of glucose, insulin and leptin, decreased FSH concentrations (P!0.01) and tended to increase oestradiol concentrations (PZ0.06). The supplement tended to increase the number of 3 mm follicles (PZ0.06). Compared with low-BC ewes, high-BC ewes had more follicular waves (P!0.05), higher concentrations of insulin, leptin and IGF1 (P!0.05) and tended to have higher FSH concentrations (PZ0.09). Leptin and insulin concentrations remained high until the end of supplementation in high-BC ewes, whereas they decreased after the third day of supplementation in low-BC ewes. In conclusion, high concentrations of metabolic hormones in fat ewes are associated with the development of more follicular waves. When a supplement is superimposed on this situation, changes in glucose and metabolic hormones allow more follicles to be selected to ovulate.

-We investigated the physiological relationship between diet during pregnancy and colostrum production in ewes to test the hypothesis that for ewes that are in low body condition, with low fat reserves, the food supply will be the main source of energy for colostrum synthesis. To this end, we measured the amount of colostrum accumulated by ewes under two levels of nutrition. We also measured the circulating concentrations of metabolites and hormones associated with lactogenesis (β-hydroxybutyrate, glucose, progesterone, prolactin, cortisol, growth hormone, leptin, insulin and insulin-like growth factor-I) Ewes were either under-fed at 70 (n = 15) or well-fed at 110% (n = 10) of their daily metabolisable energy requirement during the last two months of pregnancy. Colostrum accumulation up to parturition was 168 ± 48 g for under-fed ewes and 451 ± 103 g for well-fed ewes. After birth, under-fed ewes produced less colostrum than well-fed ewes but the difference was no longer significant. The level of nutrition also influenced the plasma concentrations of hormones and metabolites related to lactogenesis. Progesterone concentrations decreased before lambing in all animals but in under-fed ewes the fall appeared to be too small to initiate the onset of colostrum production. β-hydroxybutyrate concentrations were higher in under-fed than in well-fed ewes, suggesting that the under-fed ewes were mobilising more adipose tissue but they still did not meet their ME requirements for colostrum production. We concluded that, in underfed ewes, there are insufficient nutrients for adequate lactation and the hormone regime is inappropriate for good udder development and colostrum synthesis. udder development / lactogenesis / β-hydroxybutyrate / glucose / progesterone / prolactin / cortisol / growth hormone / leptin / insulin / insulin-like growth factor-I / lamb mortality

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