Simulation Modeling in Plant Breeding: Principles and Applications

Conventional plant breeding largely depends on phenotypic selection and breeder＇s experience, therefore the breeding efficiency is low and the predictions are inaccurate. Along with the fast development in molecular biology and biotechnology, a large amount of biological data is available for genetic studies of important breeding traits in plants, which in turn allows the conduction of genotypic selection in the breeding process. However, gene information has not been effectively used in crop improvement because of the lack of appropriate tools. The simulation approach can utilize the vast and diverse genetic information, predict the cross performance, and compare different selection methods. Thus, the best performing crosses and effective breeding strategies can be identified. QuLine is a computer tool capable of defining a range, from simple to complex genetic models, and simulating breeding processes for developing final advanced lines. On the basis of the results from simulation experiments, breeders can optimize their breeding methodology and greatly improve the breeding efficiency. In this article, the underlying principles of simulation modeling in crop enhancement is initially introduced, following which several applications of QuLine are summarized, by comparing the different selection strategies, the precision parental selection, using known gene information, and the design approach in breeding. Breeding simulation allows the definition of complicated genetic models consisting of multiple alleles, pleiotropy, epistasis, and genes, by environment interaction, and provides a useful tool for breeders, to efficiently use the wide spectrum of genetic data and information available.

Wheat breeding model for steady and high yield and early maturation in middle and south Hebei province —Analysis of steady and high yield ability of wheat variety Ji 84-5418

A wheat breeding model for high yield in the middle and south of Hebei Province was developed. Wheat variety Ji 84-5418 has been bred on this model. The analysis results of high-yield and stability indicated that Ji 84-5418 was not only an aggregate of varied excellent characters,but a recombined biotype which could early differentiate spike and develop coordi-nately,and had better self-regulation ability and potential high productivity. Its yield is stable at 6000-8250 kg/ha.

Software applications for providing comprehensive computing capabilities to problems related to mixed models in animal breeding

Several computer packages have been developed to accomplish improved programs for animal breeding and genetic selection. This paper described most of the currant software and provided suggestions for improved software. Khon Kaen University, Thailand, will provide free of charge the new software developed at Khon Kaen University by the author of this paper. The contact for requesting the software is listed: monchai@kku.ac.th.

Cost-benefit Analysis of Scale Pig Breeding in Shandong Province Based on Modified Entropy Weight-TOPSIS Model

According to the relevant statistical data in National Agricultural cost-benefit Data Compilation(2001- 2013),we use the modified entropy weight- TOPSIS model to research the cost-benefit status of scale pig breeding in Shandong Province from the perspective of comparing it with that of the entire country and 9 other main pig producing areas. The results show that compared with the national average,the cost-benefit ratio of small scale pig breeding in Shandong Province is lower,while the cost-benefit ratio of medium scale and large scale pig breeding is significantly improved; the cost-benefit ratio of small scale pig breeding in Shandong Province is basically the same as that in 9 other main pig producing areas,while the cost-benefit ratio of medium scale and large scale pig breeding is higher; the output value of main products and the purchase price of piglet are two major bottlenecks restricting the cost-benefit improvement of scale pig breeding in Shandong Province.

Porcine Breeding Management in a Large-scale Piggery with Microbial Fermentation Bed

[Objective] The behavior of eating, drinking, defecating and peeing of 1 500 pigs in a large-scale microbial fermentation bed-equipped piggery was observed. We hoped to find some simple indicators that could reflect the health status of swinery and to provide experience for the swinery performance management in large-scale microbial fermentation bed-equipped piggery. [Method] The body weight （BW）, daily BW gain, feed intake and other indicators of different-day-old pigs were recorded in details. Based on the recorded data, the models between BW, BW gain, average daily feed intake and feed/gain ratio and growth days （d） were established. In addition, the incidences of pox-like macula （dermatitis）, diarrhea （gastrointestinal disease）, cough （respiratory disease）, stiff pig （malnutrition）, conjunctivitis （eye disease） and foot inflection （trauma） among fattening pigs were also investigated. [Result] The BW range, average BW, daily BW gain, breeding days, daily feed intake range, average daily feed intake, staged feed intake, accumulated feed intake, feed/gain ratio and accumulated feed/gain ratio of different-day-old pigs were studied, respectively. Four dynamic models were established for the growth of pigs： （1） the BW （y）-age （x） mod- el： y=0.758 9x-19.883 （3=0.993 7）; （2） the BW gain （y）-age （x） model： y=1.039 5x05051 （F=0.885 4）; （3） the average daily feed intake （y）-age （x） model： y=0.023 5x-0.334 3 （F=0.991 7）; （4） the feed/gain ratio （y）-age （x） model： y=0.022x＋0.427 8 （P=0.988 5）. Based on these models, the corresponding theoretical growth value of pigs at different growth stage could be predicted. The main diseases occurred among the swinery in the large-scale microbial fermentation bed piggery included pox-like macula （dermatitis）, diarrhea （gastrointestinal disease）, cough （respiratory disease）, stiff pig （mal- nutrition）, conjunctivitis （eye disease） and foot inflection （trauma）. The deadly infec- tious diseases had been not found among the pigs. [Conclusion] When the actual BW, BW gain, average daily feed intake and feed/gain ratio were all lower than the theoretical values predicted by the models, the management should be enhanced. The average daily feed intake of 60 to 65-day-old pigs was lower than the theoretic value, indicating that the pigs could not adapt nicely to the fermentation bed at the very early stage. When the pigs grew up to 70 to 75 d old, the average daily feed intake was higher than the theoretical value, indicating that the pigs had adapted to the fermentation bed. In particularly, average daily feed intake of 75-day-old pigs was higher than the theoretical value by 21%. It was suggested the fermentation bed was conducive to the growth of pigs. Considering the occurrence of diseases among pigs, the overall incidence was relatively low. The incidence of each disease was all lower than 10% with little difficulty in treating. If the management of mattress was strength- ened, such as paying attention to feeding and keeping water clean, many diseases could heal by themselves.

Estimation of genetic parameters and breeding values in shrimp F enneropenaeus chinensis using the REML/BLUP procedure

An analysis of a selection experiment was used to assess the impact of various animal model struc- tures on REML estimates of variance components. The analyses were carried out based on 162 d body mass （BM） of 1 287 animals from 21 paternal half-sib groups of Fenneropenaeus chinensis. Estimated breeding values （EBV） of BM of all individuals were estimated using eight statistical models （A, AB, ABC, ABDC, ABMFC, ABMDC, ABFDC and ABMFDC） and BLUP （best linear unbiased prediction）. These models were designed involving factors such as sex, spawn date as fixed effects, maternal genetic effects, full-sib family effects as random effects, mean BM of families at tagging and age at recording （covariate）. The results demonstrate the importance of correct interpretation of effects in the data set, particularly those that can influence resemblance between relatives. The data structure and the particular model that was applied markedly influenced the magnitude of variance component estimates. Models based on few effects obtained upward biased estimates of additive genetic variance. The accuracy of genetic parameters and breeding value es- timated by ABFDC model was higher than other models. The results imply that additive genetic direct value, full-sib family effects, and covariance effects besides sex and spawn date as fixed effects were very important for estimating genetic parameters and breeding value of body mass. This model had a heritability estimate of 162 d BM of 0.44. The comparison of the efficiency of selection based on breeding values or phenotypic value revealed great difference： average breeding value of the best 24 families selected by the 162 d BM breeding value and phenotype were 0.577 g and 0.366 g, respectively, representing a 36.57% higher efficiency in the former. In conclusion, selection based on breeding value was more effective than selection based on phenotypic value. Our results indicate that effects influencing the magnitude of estimates should be taken into account when estimating heritability and breeding values for BM.

On Significance of Heterotic Group Theory in Hybrid Rice Breeding

Heterotic group theory （HGT） has played a major role in supporting hybrid maize breeding for about 100 years. The basic content and studies of HGT, and its application in rice and maize were summarized in this paper. Additionally, difficulties and challenges for hybrid rice breeding in China were analyzed, and necessity and urgency in hybrid rice breeding by using HGT were proposed.

Effects of breeding success,age and sex on breeding dispersal of a reintroduced population of the Crested Ibis(Nipponia nippon)in Ningshan County,China

Background: Breeding dispersal is an important ecological process that affects species' population dynamics and colonization of new suitable areas. Knowledge of the causes and consequences of breeding dispersal is fundamental to our understanding of avian ecology and evolution. Although breeding success for a wild and reintroduced population of the Crested Ibis(Nipponia nippon) has been reported, the relationships between individuals' breeding dispersal and their breeding success, age and sex remain unclear.Methods: Ibises' breeding dispersal distance, which is the distance moved by adults between sites of reproduction, was estimated based on the observations of consecutive breeding sites of marked ibis individuals. From observational and capture-recapture data(n as = 102) over 9 years, individuals' breeding dispersal probability in relation to age, sex, and reproductive success wanalyzed via a generalized linear mixed effect modeling approach.Results: Our results show that 55% males and 51% females keep their previous territories following nesting success. Failed breeding attempts increased dispersal probabilities. Both females and males failed in breeding were more likely to disperse with greater distances than successful birds(females: 825 ± 216 m vs 196 ± 101 m, males: 372 Crested Ibis exhibited a female-biased dispersal pattern that the mean dispersal distance± 164 m vs 210 ± 127 m). of females(435 ± 234 m) was much larger than that of males(294 ± 172 m).Conclusion: Our results are fundamental to predict the patterns of breeding dispersal related to reproductive success under different release sites. From the conservation point of view, landscape connectivity between the reintroduced populations should be taken into account in accordance with the distance of breeding dispersal.

Stress-Tolerant Cassava: The Role of Integrative Ecophysiology-Breeding Research in Crop Improvement

This review highlights an integrative multidisciplinary eco-physiological, breeding and agronomical research on the tropical starchy root crop cassava conducted at CIAT. Laboratory and field studies have elucidated several physio-logical/biochemical mechanisms and plant traits underlying the high productivity in favorable conditions and tolerance to stressful environments, such as prolonged water stress and marginal low-fertility soils. Cassava is endowed with inherent high photosynthetic capacity expressed in near optimal environments that correlates with biological produc- tivity across environments and wide range of germplasm.Field-measured photosynthetic rates were also associated with root yield, particularly under prolonged drought. Extensive rooting systems and stomatal sensitivity to both atmospheric humidity and soil water shortages underlie tolerance to drought. The C4 phosphoenolpyruvate carboxylase (PEPC) was associated with photosynthesis and yield making it a selectable trait, along with leaf duration, particularly for stressful environments. Germplasm from the core collection was screened for tolerance to soils low in P and K, resulting in the identification of several accessions with good levels of tolerance. Cassava has a comparative advantage against major tropical food and energy crops in terms of biological productivity. Results also point to the importance of field research versus greenhouse or growth-chamber studies. In globally warming climate,the crop is predicted to play more role in tropical and subtropical agro-ecosystems. More research is needed under tropical field conditions to understand the interactive responses to elevated carbon dioxide, temperature, soil fertility, and plant water relations.

Appropriate Scale of Breeding Cows in Family Operation of Yanbian Cattle

Family operation of breeding cow is the only way to realize modernization of animal husbandry. Through field survey of Yanbian cattle farmers, the main input indicators were analyzed, including number of breeding cows, number of breeding bulls, input of cattle house, feed cost, production equipment investment, and grazing rent. The slaughter number of store cattle per year was selected as the output index. The efficiency of family operation scale of Yanbian cattle was analyzed using BCC model of DEA. The results showed that the moderate scale of breeding cows in family operation with half grazing and half housing pattern was around 50 -60 cattle.

Breeding to Optimize Agriculture in a Changing World

Breeding to Optimize Chinese Agriculture(OPTICHINA) was a three-year EU–China project launched in June of 2011. As designed, the project acted as a new strategic model to reinforce systematic cooperation on agricultural research between Europe and China. The OPTICHINA International Conference "Breeding to Optimize Agriculture in a Changing World" was held in Beijing, May 26–29, 2014. The conference included six thematic areas:(1) defining and protecting the yield potential of traits and genes;(2) high-throughput precision phenotyping in the field;(3) molecular technologies in modern breeding;(4) plant ideotype;(5) data analysis,data management, and bioinformatics; and(6) national challenges and opportunities for China. The 10 articles collected in this special issue represent key contributions and topics of this conference. This editorial provides a brief introduction to the OPTICHINA project, followed by the main scientific points of articles published in this special issue. Finally, outcomes from a brainstorming discussion at the end of the conference are summarized, representing the authors' opinions on trends in breeding for a changing world.

Comparison of Analyses of Genetic Structure among Chinese Indigenous Chicken Breeds using Distance-based and Model-based Methods

The Nei's improved genetic distance(DA)and gene flow(Nm)were measured using sixteen microsatellite markers.Dendograms based on DA genetic distance using the neighbor-joining(NJ)method and STRUCTURE program were constructed to analyze the genetic structure and relationship among 10 Chinese indigenous chicken breeds.The results showed that dendograms of DA genetic distance using the NJ method divided the 10 chicken breeds into two main clusters;one consisted of breeds of low weight body(CHA,TTB,XIA,GUS and BAI),the other contained heavier breeds(LAN,DAG,YOU,XIS and LUY).In the lighter breeds,TIB and CHA clustered together,as did XIA and GUS.In the heavier breeds,XIS and LUY was clustered together in one branch,but LAN,DAG and YOU clustered in independent branches.The results were consistent with Nm estimates among the 10 indigenous chicken breeds.The STRUCTURE program properly inferred the presence of genetic structure despite not pre-defining the origin of individuals.The genetic cluster inferred by STRUCTURE was basically the same as that from the DA distance clustering method.An advantage of the STRUCTURE program was its ability to identify the migrants and admixed individuals in the 10 chicken populations;this could not be achieved by use of the DA distance clustering method.

我国设施生态农业主要模式及配套技术的研究与实践

设施生态农业是指在设施种植和设施养殖中采用清洁、绿色、健康生产方式,以提高资源利用效率、农产品产量与质量、环境效益为目标的生态农业模式。2002年农业部重点推广的设施生态农业模式主要有两大类:一类是种养沼三结合的“四位一体”生态模式,从最初以农户为单位的单体日光温室到以村庄为单位的种养结合生态温室群模式,拓展到在一个大区域内将大型猪场的粪污进行工业化沼气并网发电,沼液通过管道输送到农田来减少化肥施用和改良土壤的宏观生态农业模式,相关的结构配置、配套的种养殖技术和装备也在不断研发和提升中。另一类是采用综合性生态农业技术的设施生态农业模式,包括:采用各类立体/垂直栽培技术提高土地资源利用率;通过各种轮作栽培技术减少设施蔬菜土壤连作障碍和降低农药使用量;采用土壤健康栽培技术,通过有机肥的合理施用改善土壤性状;采用有机基质栽培技术,用农林废弃物发酵后的物料作为栽培基质为作物提供养分;采用覆盖防虫网、色板诱杀、灯光诱杀、高温封棚、蒸气消毒、有色膜覆盖土壤、天敌昆虫生物防治等病虫草害生态防治技术来减少有害生物发生。期望通过相关配套装备技术的进一步研发提高设施生态农业的信息化、自动化水平,实现设施农业的可持续发展。

碳约束下不同规模生猪养殖技术效率及贡献率测度

为了解决生猪养殖主体追求效益最大化和环境保护之间的冲突,度量碳约束下的生猪养殖技术效率,本研究以我国生猪养殖大省四川省、河南省、山东省、云南省、湖北省、广东省及广西壮族自治区为研究对象,选取2012—2021年4种生猪养殖规模投入产出的面板数据,采用超对数随机前沿模型对4种养殖规模下生猪养殖的技术效率及各生产要素的贡献率进行分析。结果表明:碳约束对散养、小规模和中规模养殖的技术效率具有显著影响,而对大规模养殖的技术效率影响不显著;中规模是生猪养殖生产前沿面的分界规模,当养殖规模低于中规模时,技术效率明显降低;当养殖规模为中规模时,技术效率明显提高;养殖规模对技术进步贡献率存在“U”型影响,小规模是“U”型拐点。说明我国应推广中、大规模养殖,其中小规模向中规模过渡时,应重点增加人工投入;中规模向大规模过渡时,应增加创新投入,提高技术进步贡献率。

苏中地区蛋鸡养殖碳排放估算与技术效率分析

为应对当前畜牧业减排形势,促进蛋鸡养殖业健康持续性发展,研究以江苏省中部地区133个蛋鸡养殖场为研究对象,运用生命周期评价法计算蛋鸡养殖全过程碳排放的情况,利用SBM(Slack based measure)模型从经济与环境角度探究蛋鸡养殖的技术效率。结果显示:该地区只均蛋鸡在整个生命周期中的碳排放为48.55 kg,其中粪便处理是影响碳排放结果的最主要因素,占总排放量的38%。该地区蛋鸡养殖环境效率为0.619 4,低于技术效率(0.667 5),环境效率和技术效率都有较大的提升空间。通过降低投入冗余,只均蛋鸡碳排放量可降低约9.03 kg。蛋鸡养殖具有一定的环境污染性,不同规模之间的蛋鸡养殖效率差异较大,中规模养殖场有明显的环境效率优势。

新疆肉羊产业发展现状及未来养殖模式展望

新疆是羊肉的重要生产地和消费地,肉羊产业对新疆农牧业增效及农牧民增收致富具有重要意义。当前新疆地区羊肉供给严重不足,满足不了当地消费需求,养殖模式与方法相对分散与落后,与现代化、集约化养殖模式存在很大差距。该文分析了新疆肉羊产业的发展现状及面临的挑战和问题,探讨发展肉羊智慧化养殖的趋势及意义,对新疆肉羊产业发展智慧养殖的前景进行了展望,并提出发展标准化规模养殖、加强科技队伍建设、完善科技支撑体系、加快饲草料产业发展、推广智慧化养殖技术、打造规模化羊场智慧管理云平台等建议,为新疆肉羊产业健康、可持续发展提供参考。

中国蛋鸡饲养绿色全要素生产率实证研究

为提高蛋鸡生产效率的同时减少污染排放,在考虑负向产出以及规模异质性和地区异质性的前提下,对蛋鸡养殖绿色全要素生产率(LHBG)进行测度。构建3层次SBM-MML指数,并将其分解为规模结构效率、技术效率以及管理效率。结果表明,2004-2018年平均LHBG为0.9967;大中小规模LHBG分别为0.9949、1.0013、0.9938;东中西部地区LHBG分别为0.9930、0.9980、1.0040。我国蛋鸡饲养绿色全要素生产率总体下降0.33%;规模上中规模最高、大规模其次、小规模最低;区域上西部最高,中部其次,东部最低;其分解效率表现为规模结构效率和技术效率提高,管理效率下降。

面向农作物种质资源智能化管控与应用的本体构建

[目的/意义]以“生物技术+人工智能+大数据信息技术”为特征的育种4.0对种质资源的数字化管控与智能利用提出了新需求。为满足智能背景下对知识服务形态多样化的支持需求,文章旨在提出一种有效知识化组织、深度语义关联的方法。[方法/过程]通过分析领域数据描述及组织现状,参考作物本体、达尔文核心,融合《农作物种质资源技术规范》和实例数据,构建了覆盖粮食、经济等五大类农作物的本体模型,定义表型、基因型等11个核心类、10个对象属性和56个数据?属性。[结果/结论]基于该本体模型,文章提出农作物种质资源知识图谱构建思路,以及知识图谱驱动的智能问答、知识计算等新型智能化知识服务场景设计展望,以期为计算育种工作提供更加准确和高效的支持,为新质生产力的创新提供参考。

作物全基因组选择育种技术研究进展

全基因组选择(GS)育种是根据训练群体全基因组上的分子标记基因型和表型之间的关联构建遗传模型,进而对基因型已知的待选群体进行育种值估计或表型预测,以实现对育种群体高效和精确的选择。相比于常用的分子标记辅助选择育种,GS育种无需进行标记显著性测验,特别适用于微效多基因控制的数量性状,可以缩短育种周期,降低育种成本,现已成为动、植物育种领域的一项前沿技术。然而,对受环境影响较大的作物产量等数量性状而言,仍面临着基因组预测准确性难以提升的瓶颈问题。本文首先分析了影响作物GS功效的主要因素,继而从非加性效应模型、群体构建方案、多性状与多环境预测、多组学预测和育种芯片技术现状等方面阐述了GS技术在作物育种中的研究进展,并指出研究所面临的问题和发展前景,为推动作物GS育种技术的进一步深入研究提供策略和思路。

基于BLUP-GGE双标图的白桦子代多地点速生性及稳定性分析

【目的】通过白桦子代多地点试验,分析其速生性和稳定性,筛选出优良家系,为种子园的改建和重建提供科学依据。【方法】以3个试验点的8年生白桦半同胞家系子代试验林为研究对象,调查其树高、胸径、材积、通直度、保存率性状,采用R语言中的ASReml-R4.0软件包,拟合具有异质方差的混合线性模型,通过最佳线性无偏预测法(BLUP)获得不同试验点各家系的综合育种值,并结合GGE双标图对各参试点和家系进行综合评价及选择。【结果】(1)以地点为固定效应的混合线性模型分析中,白桦半同胞家系子代的5个性状在地点间、家系间、以及地点×家系的互作间的差异均达到显著水平(P<0.05,Z ratio>1.5)。(2)基于各家系综合育种值的GGE双标图显示,尚志试验点的区分度和代表性均最优,庆安和尚志试验点的相关性最强,永吉与尚志试验点几乎不相关、与庆安试验点负相关。(3)16号和15号白桦家系的速生性最优,4号和32号白桦家系的稳定性最强。基于各家系速生性和稳定性的综合性状排序,按20%的入选率共选出16号、40号、15号和38号4个优良家系。【结论】白桦半同胞家系在不同试验地点的生长表现存在显著差异,同一试验地点内不同家系之间的生长表现也存在差异。基因型(家系)与环境(地点)的交互作用对白桦的生长有显著影响。依据各家系速生性及稳定性综合性状,选出16号、40号、15号和38号为白桦半同胞优良家系。