Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus

To further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution. The 16% of all SNPs located in significant differentially used TSS clusters across sub-species had significant shifts in allele frequency (472 SNPs), indicating they may have been subject to selection. In spleen and muscle, a higher relative TSS expression was observed in Bos indicus than Bos taurus for all heat shock protein genes, which may be responsible for the tropical adaptation of Bos indicus.

Author Correction: Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Genotypic Performance of Short-Day Runner Bean (Phaseolus coccineus L.) Lines Combining High Grain Yield and Disease Resistance

Runner bean (Phaseolus coccineus L.) offers a great potential as a grain legume in Africa. However, its productivity is low because no improved short-day varieties are available. The aim of this study was to evaluate advanced short-day runner bean lines for high grain yield, resistance to diseases and suitable for cultivation under tropical conditions. F6.8 recombinant inbred lines developed from crosses between local landraces and high yielding imported variety (White Emergo) were evaluated in 2013 and 2014 in a randomized complete block design with three replicates at Kabete (1860 m.a.s.l.) and Ol Joro-Orok (2300 m.a.s.l.) in Kenya. Four local runner bean landraces were used as checks. Analysis of variance showed that there were significant differences for days to flowering, response to diseases and grain yield among the evaluated lines. Improved lines flowered within 49 to 52 days in 2013 and 34 to 58 days in 2014.The improved lines flowered earlier at Kabete than Ol Joro-Orok and showed a higher degree of resistance (scores 1-3) to the major diseases rust, bean common mosaic virus (BCMV) and powdery mildew. The mean grain yield at Kabete was 4,426 kg ha-1 compared to 6,523 kg ha-1 at Ol Joro-Orok giving an average yield advantage of up to 67% compared with local short-day landraces. The results indicated that new high yielding short-day runner bean varieties with resistance to major diseases and tropical adaptation can be obtained from these lines.

Genetic relationships of female reproduction with growth, body composition, maternal weaning weight and tropical adaptation in two tropical beef genotypes

The genetic relationships of female reproduction with growth and body composition, tropical adaptation traits and maternal weaning weight (descriptive of genetic potential milk production) were estimated in 1027 Brahman (BRAH) and 1132 Tropical Composite (TCOMP) females. Female reproduction was evaluated at puberty, as outcomes of the first and second annual mating periods (Mating 1 and Mating 2, which commenced when females averaged 27 and 39 months of age, respectively), as well as annual averages over up to six matings. Traits evaluated included age at puberty, Mating 1 and 2 pregnancy rate, weaning rate and days to calving, and lifetime annual calving and weaning rate. Traits describing growth and body composition (liveweight, hip height, ultrasound-scanned P8 fat depth and eye muscle area, subjective body condition score and blood IGF-I concentration) were measured in the animals as heifers (at ~18 months of age), and again at the start of Mating 2. Traits describing tropical adaptation included coat-length scores in both genotypes and, in BRAH, buffalo fly lesion scores. Previously reported analyses of these data identified heifer IGF-I and coat and buffalo-fly-lesion scores as potential genetic indicators for age at puberty in BRAH. The results of the present study found that exploiting these relationships would have no unfavourable genetic consequences for later female reproduction and, in some cases, may be indicators of female reproduction, when evaluated as outcomes of Matings 1 or 2, or as lifetime annual calving or weaning rates. For BRAH, heifer liveweight was a genetic indicator for Mating 1 weaning rate (rg = 0.70), and, while standard errors were high, there were also positive genetic correlations of heifer hip height, eye muscle area and blood IGF-I concentration with Mating 1 weaning rate (rg = 0.61, 0.58 and 0.43, respectively). For TCOMP, significant genetic relationships of heifer growth, body composition and tropical adaptation traits with female reproduction were virtually absent, suggesting that there is less opportunity to identify earlier in life measures as genetic indicators of reproduction for this genotype. Higher maternal weaning weight was significantly genetically related to lower lifetime annual weaning rate (rg = –0.50) in BRAH, and with lower Mating 2 calving and weaning rate (rg = –0.72 and –0.59, respectively) in TCOMP, which will need to be considered when making selection decisions that affect genetic milk in these genotypes. Importantly, the results presented revealed no strong genetic antagonisms of heifer growth and body composition traits with female reproduction, suggesting that selection could be undertaken to improve these simultaneously.

Application of physiological understanding in soybean improvement. II. Broadening phenological adaptation across regions and sowing dates

This paper describes the implementation of a strategy to develop high-yielding soybean cultivars with wider adaptation across latitudes and sowing dates using the ‘long juvenile’ (LJ) trait to ‘convert’ elite temperate cultivars to subtropical and tropical adaptation. In an initial proof-of-concept evaluation, temperate semi-dwarf cultivars from Ohio in the Mid-West of the USA (40°N) were converted into genotypes adapted to the subtropics of southern Queensland (25–28°S), of which cv. Melrose was the first to be released for commercial production. The effect of the LJ trait was to delay flowering of the new genotypes by 10–14 days depending on temperature, while retaining the high yield potential and lodging resistance of the temperate varieties. The temperate cultivars were insensitive to photoperiod in the subtropics, and this attribute was largely retained in cv. Melrose. The LJ trait was also used to convert temperate culinary soybean varieties from eastern Asia to subtropical–tropical adaptation, although susceptibility to disease required the simultaneous introgression of resistance genes from additional sources. Several elite LJ oilseed and culinary varieties with broad adaptation in eastern Australia have since been developed. Like Melrose, these varieties are earlier maturing (110–125 days duration) than traditional, full-season cultivars (120–140 days depending on sowing date), less sensitive to photoperiod, and require higher plant populations than full-season varieties for maximum yield. However, they can be grown over a wider range of latitudes and sowing dates than full-season varieties. Similarly, the LJ trait was used to delay flowering of very early flowering, photoperiod-insensitive soybean varieties used in Asian farming systems, increasing yield potential without changing photoperiod insensitivity. The broadening of varietal adaptation over latitudes and sowing dates has allowed public soybean breeding resources to be rationalised, with one national Australian program replacing four previous, regionally focused programs. The research provides a tangible example of how physiological understanding of genotype × environment interaction contributed to soybean improvement in eastern Australia.