Identification of potential genomic regions for egg weight by a haplotype-based genome-wide association study using Bayesian methods

ABSTRACT

1. Theoretically, haplotype blocks might be a more suitable alternative to SNP genotypes as they are usually better at capturing multi-allelic QTL effects, compared to individual SNP genotypes in genome-wide association studies. The objectives of this study were to identify genomic regions related to egg weight traits by Bayesian methods (BayesA, BayesB, and BayesN) that fit fixed-length haplotypes using GenSel software.

2. Genotypes at 294,705 SNPs, that were common on a 600K Affymetrix chip, were phased for an egg-laying hen population of 1,063 birds. Recorded traits included first egg weight (FEW) and average egg weight at 28, 36, 56, 66, 72 and 80 weeks of age.

2. Fitting 1Mb haplotypes from BayesB resulted in the highest proportion of genetic variance explained for the egg weight traits. Based on the trait, the genetic variance explained by each marker ranged from 27% to 76%.

3. Different haplotype windows associated with egg weight traits only explained a small percentage of the genetic variance.

4. The top one 1-Mb window on GGA1 explained approximately 4.05% of total genetic variance for the FEW. Candidate genes, including PRKAR2B, HMGA2, LEMD3, GRIP1, EHBP1, MAP3K7, and MYH were identified for egg weight traits.

5. Several genomic regions, potentially associated with egg weight traits, were identified, some of which overlapped with known genes and previously reported QTL regions for egg production traits.     

小麦秸秆长度、覆盖量对坡面产流产沙的影响

为定量研究小麦秸秆覆盖对坡面产沙产流过程及减水减沙效益的影响,采用室内人工模拟降雨试验,研究在降雨强度为90 mm/h时,不同秸秆长度和秸秆覆盖量下的坡面产流产沙特征和产流产沙过程规律,结果表明:(1)在相同秸秆长度下,随秸秆覆盖量增加,产流量产沙量极显著减少(p0.01)。相同覆盖量水平下随秸秆长度增加,产流量显著增加(p0.05),在4.5 t/hm~2覆盖量下产沙量极显著增加(p0.01)。(2)秸秆覆盖坡面的初始产流时间较裸露坡面延迟6.23倍,产流量平均下降19.5%,产沙量下降31.6%。覆盖措施通过保护土壤的结构有效抑制了细沟侵蚀过程向切沟侵蚀发展。产流产沙过程受秸秆长度和覆盖量的交互作用影响,交互效应对产流过程的影响更突出。(3)随覆盖量增加,减水减沙效益极显著增加(p0.01);随长度增加,减水减沙效益分别减少为17.26%,27.97%。不同覆盖条件下的坡面产流量、产沙量和减水、减沙效益均与秸秆长度、秸秆覆盖量呈二元线性关系。(4)在当前试验条件下,当秸秆长度为3～5 cm,覆盖量为4.5 t/hm~2时达到最优减水减沙效益。     

Intensive organic vegetable production increases soil organic carbon but with a lower carbon conversion efficiency than integrated management

Intensive vegetable production in greenhouses has rapidly expanded in China since the 1990s and increased to 1.3 million ha of farmland by 2016, which is the highest in the world. We conducted an 11‐year greenhouse vegetable production experiment from 2002 to 2013 to observe soil organic carbon (SOC) dynamics under three management systems, i.e., conventional (CON), integrated (ING), and intensive organic (ORG) farming. Soil samples (0–20 and 20–40 cm depth) were collected in 2002 and 2013 and separated into four particle‐size fractions, i.e., coarse sand (> 250 µm), fine sand (250–53 µm), silt (53–2 µm), and clay (< 2 µm). The SOC contents and δ¹³C values of the whole soil and the four particle‐size fractions were analyzed. After 11 years of vegetable farming, ORG and ING significantly increased SOC stocks (0–20 cm) by 4008 ± 36.6 and 2880 ± 365 kg C ha^?1 y^?1, respectively, 8.1‐ and 5.8‐times that of CON (494 ± 42.6 kg C ha^?1 y^?1). The SOC stock increase in ORG at 20–40 cm depth was 245 ± 66.4 kg C ha^?1 y^?1, significantly higher than in ING (66 ± 13.4 kg C ha^?1 y^?1) and CON (109 ± 44.8 kg C ha^?1 y^?1). Analyses of ¹³C revealed a significant increase in newly produced SOC in both soil layers in ORG. However, the carbon conversion efficiency (CE: increased organic carbon in soil divided by organic carbon input) was lower in ORG (14.4%–21.7%) than in ING (18.2%–27.4%). Among the four particle‐sizes in the 0–20 cm layer, the silt fraction exhibited the largest proportion of increase in SOC content (57.8% and 55.4% of the SOC increase in ORG and ING, respectively). A similar trend was detected in the 20–40 cm soil layer. Over all, intensive organic (ORG) vegetable production increases soil organic carbon but with a lower carbon conversion efficiency than integrated (ING) management.     

Unravelling the relationship between a seasonal environment and the dynamics of forage growth in grazed swards

It is well reported in the scientific literature that pastures can have similar net forage accumulation when managed with contrasting structures. However, we hypothesized that the dynamics of forage accumulation in grazed swards is linked to seasonal-environmental conditions. Marandu palisadegrass (Brachiaria brizantha [Hochst. ex A. Rich.] was used as the forage species model. The experimental treatments were four grazing heights (10, 20, 30 and 40 cm) allocated to experimental units according to a randomized complete block design with four replicates and evaluated throughout four contrasting environmental seasons (summer, autumn, winter–early spring and late spring). Under rainy and warm periods, greater net forage accumulation was observed in pastures maintained taller; on the contrary, during the mild and dry periods, net forage accumulation rate reduced as grazing height increased. Such patterns of responses were related to compensations between tiller population density and tissues flows during summer and late spring and the reduced capacity of taller canopies to compensate lower population with greater growth rates during autumn and winter–early spring. Grazed swards changed their patterns of forage growth as they transitioned from favourable to more abiotic stressful conditions, suggesting that seasonal adjustments in grazing intensities are necessary in order to maximize forage production.     

Influence of Aguamiel (Agave atrovirens) as a Natural Feed Additive on Cecal Fermentation Kinetics of Some Forage Species in Horse Feeding

This study aimed to evaluate the effect of different dose levels of aguamiel (Agave atrovirens) on in vitro cecal gas, methane (CH₄), and carbon dioxide (CO₂) productions of five forage species (Avena sativa [hay]), Moringa oleifera, Caesalpinia coriacea, Salix babylonica, and Eichhornia crassipes using inocula from the horse. The forage samples were incubated with three doses of aguamiel: 0, 34, and 68 μg of aguamiel/g dry matter (DM) of substrate. Cecal inocula were collected from four adult female Criolla horses (3–4 years of age and weighing 300 ± 15.0 kg) grazed on native grasses for about 8 hours without supplementation. Forage type affected (P < .001) cecal asymptotic, rate and lag time of gas, CH₄ and CO₂ productions (mL/g DM), pH and DM degradability. Aguamiel dose had linear and quadratic effects (P < .05) on the asymptotic and rate of CH₄ productions and rate and lag time of CO₂ productions (mL/g DM). Forage type × aguamiel dose interactions were significant (P < .05) for asymptotic, rate and lag time of gas, and CH₄ and CO₂ productions (mL/g DM). Forage species effects were pronounced (P < .05) on CH₄ and CO₂ productions (mL/g incubated and degraded DM) and proportional CH₄ production at all hours of incubation, except for CO₂ production (mL/g incubated DM). Aguamiel dose affected (P < .05) CO₂ production (mL/g incubated DM) and proportional CO₂ production at the incubated hours. Forage type × aguamiel dose interactions were observed (P < .05) for CO₂ production (mL/g incubated DM) and proportional CO₂ production at the incubated hours but had no impact on CH₄ production. It is concluded that addition of aguamiel to five forage species affected fermentation kinetics of gas production resulting in different in vitro cecal gas, CH₄ and CO₂ productions from these substrates.     

湖南粮食生产区域布局优化战略

在综合分析资源禀赋、技术条件、市场区位、生产规模、产业基础及布局指向等方面因素，兼顾相对集中连片原则，结合粮食生产现状、市场前景与产业发展趋势的基础上，提出了将湖南划分为“一区一圈两带”的粮食生产区域布局优化战略。对“一区一圈两带”4个片区的粮食生产特征进行了总结，并提出了各片区的功能定位和主攻方向。     

劳动力老龄化对我国农业生产效率的影响

针对我国农村人口老龄化现象不断加剧,致使农业劳动力供给质量下降等问题,以2009年农村固定观察点数据为依据,分析我国农业劳动力老龄化现状,并利用柯布道格拉斯生产函数研究劳动力老龄化对农业生产效率的影响。结果表明:我国农业生产中存在严重的老龄化现象,60岁以上的劳动力占18.42%;与年轻劳动力相比,老龄劳动力的生产效率明显较低,老龄农户不仅主要生产要素的边际产值低于非老龄农户,而且耕种面积以及其他各生产要素的投入水平也均低于非老龄户,这说明农业老龄化严重制约着我国农业的发展。     

Optimisation of fertiliser rates in crop production against energy use indicators

Optimising mineral nitrogen (N) use in crop production is inevitable target as mineral fertilisers reflect one of the highest inputs both in terms of economy and energy. The aim of the study was to compare the relationship between the rate of N fertiliser application and different measures of energy parameters exemplary data for spring-wheat in boreal climate condition in Estonia in 2006–2010. The effect of mineral N with rates 0, 40, 80, 120 and 160 kg N ha⁻¹ was studied on the background of composted cow manure and without organic fertilisers. Univalent parameters, energy gain (EG) (energy output − energy input) and energy ratio (ER) (energy output/energy input) were calculated. To aggregate parameters with different units (ER and EG) we proposed two standardisation approaches for combined indices. ER maximisation gave both organic fertilisation background optimum N norms significantly lower than EG (p < 0.05) optimisation. Both the new combined indices gave optimum N norms in between the rate of ER an EG. Composted cow manure background did not affect mineral N optimisation significantly. We suggest optimisation of mineral N according to bi-dimensional parameters as they capture important features of production efficiency and are more objective using as advisory tool for sustainable production systems.     

中国畜牧业生产波动的特征及路径识别

基于1978—2016年畜禽产品年度产量数据,采用HP滤波技术和非线性MS-AR模型,分析中国畜牧业生产波动的特征,从畜牧业生产区制转换的视角剖析畜牧业生产波动的具体路径,探讨影响畜牧业生产波动和路径转换的原因。结果表明:从生产波动变化趋势上看,猪肉生产增长高峰期出现最早,其次是牛肉、羊肉、禽肉和禽蛋生产,牛奶生产增长高峰期出现时间最晚;从生产波动比较上看,猪肉生产波动幅度最小,其他畜牧产业生产波动幅度相对较大,各畜牧产业生产波动趋势存在差异,但近年来总体趋于收敛。通过模型识别将畜牧业生产划分为低速、中速和快速增长3个区制,低速和中速增长区制下各畜禽业产品产量平均增长率在3%和5%左右,而快速增长区制下平均增长率在10%以上;猪肉生产倾向于保持中速增长,牛肉、羊肉和牛奶生产容易出现低中速增长往复徘徊的现象,禽肉和禽蛋生产在各区制下均较为稳定且区制变迁较为平稳;改革开放以来,除牛奶产业以外,其他畜牧产业生产基本在低速或中速增长区制时间最长。基于此,提出针对不同畜禽产业在不同发展阶段相机制定不同调控政策,推动畜禽产业规模化养殖和产业化经营水平,提高畜禽产业抗冲击能力等建议。