Genetic diversity evolution through participatory maize breeding in Portugal

Natural, and in particular, artificial (human) selection may pose a danger to the existing crop genetic diversity. Nevertheless, on-farm breeding systems seem to achieve phenotypic improvements even though preserving variability. Using SSR markers, we analysed several selection cycles, over a 20 years period, of a Portuguese on-farm participatory maize OPV-‘Pigarro’ breeding project. No significant differences in allelic richness (N_ar), observed heterozygosity (H_O), expected heterozygosity (or gene diversity; H_E) or inbreeding coefficient (f) were detected among the selection cycles. 58 out of 107 alleles were common to all the selection cycles studied. The analysis of molecular variance showed that the variation among selection cycles represented only 7% of the total molecular variation. However, the number of private alleles varied among the selection cycles, being the highest detected at the beginning of the selection project. These findings demonstrate that an allele flow took place during the on-farm selection process of ‘Pigarro’ but the level of genetic diversity was not significantly influenced. Since interesting phenotypic improvements were also achieved, on-farm breeding projects, like this one, should be valued as a way to preserve unique Portuguese maize landraces in risk of disappearing.     

Genomic analysis of maize lines introduced in the early stages of a breeding programme

The diversity analysis and screening of major genes using genomewide association studies (GWAS) for quantitative traits have been exploited in several grass crops, but in maize it has been neglected. This study was conducted to evaluate the genetic diversity of a collection of lines and the potential of genomic analysis as an initial screening tool. For this purpose, a collection of 470 maize inbred lines were genotyped with 23,153 Dart‐seq markers. The genomewide analysis of ear weight was used aiming to perform an initial screening in our germplasm. The diversity analysis allowed the lines to be separated into distinct groups, and most of the lines were in agreement with previous pedigree information. The GWAS revealed ten regions potentially associated with the ear weight trait, one of which was related to drought stress. The results of a multiple marker analysis confirmed four of these regions, presenting a predictive accuracy of 0.6. Based on the molecular data and the results of GWAS, it is possible to infer the potential use of this genetic background for breeding.     

不同轮回选择方法对玉米窄基群体的改良效果

利用轮回选择进行群体改良,是玉米种质扩增与改良的有效方法,能为选育优良自交系提供基本素材,进而提高选育自交系及杂交种的效率。本研究以玉米窄基群体P4C0及其经过不同轮回选择方法改良的10个群体为材料,通过多点田间表型鉴定和配合力测定,研究不同轮回选择方法对玉米窄基群体的改良效果,利用SSR分子标记分析不同轮回选择方法对群体遗传多样性的影响。结果表明,几种轮回选择方法都能有效改良群体的主要性状及其一般配合力(GCA)。以时间计算,控制双亲混合选择(MS)对群体P4C0主要性状及其GCA改良效果优于半同胞-S2:3(HS-S2:3)轮回选择,但在株高和穗位高的改良上,HS-S2:3选择效果较好。以轮次计算,开放改良对群体P4HSC1主要性状及其GCA的改良效果优于MS,但开放改良后,群体株高和穗位高有较大幅度的增加。不同轮回选择方法对群体遗传多样性和遗传结构的影响不尽一致。P4C0经过5轮MS后,在群体改良的低代,群体遗传多样性得到了较好的保持,而多代的改良导致群体遗传多样性下降;P4C0经过1轮HS-S2:3选择后,遗传多样性比P4C0有较大幅度的下降。P4HSC1经过1轮开放改良后,遗传多样性有较大幅度的增加。P4HSC1经过3轮MS改良后,群体遗传多样性呈增大的趋势,但每轮增加的幅度均较小。     

QTL mapping for six ear leaf architecture traits under water‐stressed and well‐watered conditions in maize (Zea mays L.)

Morphological traits for ear leaf are determinant traits influencing plant architecture and drought tolerance in maize. However, the genetic controls of ear leaf architecture traits remain poorly understood under drought stress. Here, we identified 100 quantitative trait loci (QTLs) for leaf angle, leaf orientation value, leaf length, leaf width, leaf size and leaf shape value of ear leaf across four populations under drought‐stressed and unstressed conditions, which explained 0.71%–20.62% of phenotypic variation in single watering condition. Forty‐five of the 100 QTLs were identified under water‐stressed conditions, and 29 stable QTLs (sQTLs) were identified under water‐stressed conditions, which could be useful for the genetic improvement of maize drought tolerance via QTL pyramiding. We further integrated 27 independent QTL studies in a meta‐analysis to identify 21 meta‐QTLs (mQTLs). Then, 24 candidate genes controlling leaf architecture traits coincided with 20 corresponding mQTLs. Thus, new/valuable information on quantitative traits has shed some light on the molecular mechanisms responsible for leaf architecture traits affected by watering conditions. Furthermore, alleles for leaf architecture traits provide useful targets for marker‐assisted selection to generate high‐yielding maize varieties.     

Evaluation of three cycles of full-sib reciprocal recurrent selection in two maize populations from the Northeast of Spain

In Europe a heterotic pattern commonly used in maize breeding is “American Dent × European Flint”. Maize breeding programs generally use only a small portion of the useful genetic variability present in the local open-pollinated varieties which, otherwise, have a poor performance that hampers their use. Two maize composites, EZS33 formed by open-pollinated flint varieties from dry or Mediterranean Spain, and EZS34 from USA dent populations, were developed in Zaragoza (Spain). Both were subjected to three cycles of full-sib reciprocal recurrent selection (RRS) for yield. The objective of our study was to evaluate after three cycles of selection the effect of RRS. The selection significantly increased yield in the population crosses (3.0 % per cycle) and in the crosses of the populations with testers of different origin. The correlated responses for the population crosses in other agronomic traits like flowering and early vigor were in the desired direction, but plant height was reduced. We propose that stover yield or related traits could be included in selection programs as selection criteria to prevent their decline. The adapted population increased the frequency of favorable alleles for yield, but the inbreeding depression counteracted their effect on the mean. RRS had a positive effect on other traits. According to our data, RRS can be useful to develop improved populations from which it would be possible to develop lines with improved both specific and general combining ability with different heterotic groups. We conclude that the heterotic pattern “Mediterranean Spain × US Dent” is potentially very useful for maize breeding for adaptation to Mediterranean conditions and an interesting source of cultivars for low-input agriculture.     

Genetic mapping of quantitative trait locus for the leaf morphological traits in a recombinant inbred line population by ultra-high–density maps across multi-environments of maize (Zea mays)

Leaf is the main organ of photosynthetic reaction of plants. Studying the genetic mechanism that affects the leaf shape is very important for the improvement of maize production. In this study, a RIL population, derived from a cross between Ye478 and Qi319, was planted in four different environments, and six leaf morphological traits were measured, including the leaf angle of first leaf above ear, the leaf angle of first leaf below ear, leaf orientation value, leaf area of first leaf above ear, leaf area of ear and leaf area of first leaf below ear. By combining with a genetic map containing 4,602 bin markers, 39 QTLs associated with leaf morphological traits were identified. Among them, four QTLs explained more than 10% of the phenotypic variance, and the QTL qLOV8-2 which controlled LOV not only had a phenotypic contribution rate of 13.86% but also was detected in four environments, which could be considered as a stable major QTL. These results provide useful information for understanding the molecular mechanisms controlling maize leaf morphological traits.     

不同密度下玉米穗部性状的QTL分析

为研究玉米穗部性状对不同种植密度的遗传响应,以郑58和HD568为亲本构建的220个重组自交系群体为材料,于2014年春、2014年冬及2015年春分别在北京和海南进行3个种植密度的田间试验,调查玉米穗长、穗粗、穗行数和行粒数等表型性状。利用SAS软件计算穗部性状的最优线性无偏估计值(BLUP),并采用完备区间作图法进行QTL定位。结果表明,在3个种植密度下共检测到42个QTL,单个QTL可解释4.20%~14.07%的表型变异。3个种植密度下同时检测到位于第2染色体上控制穗行数的QTL。2个种植密度下同时检测到4个与穗粗、穗行数和行粒数有关的QTL,其中第4染色体上1个与穗行数有关的主效QTL,在低、中种植密度下可分别解释表型变异的10.88%和14.07%。此外,在第2、4和9染色体上检测到3个同时调控不同穗部性状的QTL。研究结果表明玉米穗部性状在不同种植密度下的遗传调控发生变化,在不同密度下共同检测到的稳定QTL可应用于精细定位或开发玉米耐密性分子标记用于辅助育种。     

Participatory plant breeding with maize in Mexico and Honduras

Maize is a staple food crop in many developing countries. However, if seven major maize producing countries are excluded from this group, data indicate that only 34% of the maize area is planted with improved seed despite considerable effort invested in maize breeding. This has led researchers to investigate other options, such as farmer-participatory plant breeding, for delivering the benefits of plant breeding knowledge and technology to farmers in developing countries. This paper describes short-term results from participatory maize breeding studies in Mexico and Honduras. Results from three selection cycles in Mexico suggest that stratified mass selection without pollination control, with selections carried out by researchers in farmers' fields, may be effective at improving yield in farmers' local varieties. In Honduras, mass selection with pollination control, where selections were done by collaborating farmers in their own fields on their own varieties, showed trends (non-significant) towards yield improvement. Farmer selection seemed to offer the greatest yield benefit over experiment station selection on the farm with the lowest yield potential, suggesting that farmer-participatory approaches may be most advantageous in marginal environments where experiment station conditions differ most dramatically from farmers' conditions. These studies highlighted the importance of seed systems knowledge in designing participatory plant breeding programs. For cross-pollinated crops, they also highlighted the need to balance progress from selection and demands on farmers' time and labor in choosing breeding methods. Further work is needed to investigate farmer-participatory breeding approaches that can address post-harvest traits. This revised version was published online in August 2006 with corrections to the Cover Date.     

分子标记技术在家畜育种中的应用

为了将分子标记技术更好的应用到家畜育种工作中。本文详细总结了分子标记技术在家畜遗传多样性分析、亲缘关系分析、遗传图谱构建、基因定位、杂种优势预测、性别鉴定和抗病育种等诸多方面的应用研究。提出应将表型性状、系谱和分子标记三者结合应用于家畜遗传育种等方面的工作。     

控制双亲混合选择对不同玉米合成群体的改良效应

基于田间试验的统计分析和SSR分子标记的遗传参数评估,分析了3个玉米人工合成群体GP3、GP4和GP5经4轮控制双亲混合选择的改良效应。结果表明,多数性状在不同群体及不同轮回间存在真实的遗传差异,粒深遗传增益以GP4＞GP5＞GP3,穗行遗传增益以GP3＞GP5＞GP4,各个群体C4的粒深、穗行均值都显著或极显著大于C0,直接选择效应显著;株高和穗位高随选择周期增加呈明显增加趋势,且GP4的增幅显著大于GP3和GP5,单株产量及穗粗的遗传增益以GP4大于GP3和GP5,各群体多数产量性状的均值以C4显著大于C0,相关选择效应显著;除株高、穗位高外,其他性状GCA变异群体间差异达显著或极显著水平,GP5多数产量性状的GCA优于GP3和GP4,各群体多数产量性状的GCA效应值随改良进展呈增加趋势,对照优势大于8%的大部分测交组合均为各群体C4所配组合,间接选择效应显著;随改良世代进行,群体部分性状的表型变异系数虽有所减小,但变化幅度不大;基于SSR分子标记估算的群体内遗传相似系数,GP3和GP4改良后代呈略增趋势,GP5变化不大,对于群体基因型数,GP3和GP4随改良代数增加呈略减趋势,GP5呈略增趋势。上述结果说明,适度控制双亲混合选择在有效改良群体的同时,还能较好地保持群体的遗传多样性,但不同基础群体及不同性状间,其改良效应存在一定的差异。     

Genomic selection and enablers for agronomic traits in maize (Zea mays): A review

Maize is a commodity crop providing millions of people with food, feed, industrial raw material and economic opportunities. However, maize yields in Africa are relatively stagnant and low, at a mean of 1.7 t ha⁻¹ compared with the global average of 6 t ha⁻¹. The yield gap can be narrowed with accelerated and precision breeding strategies that are required to develop and deploy high-yielding and climate-resilient maize varieties. Genomic and phenotypic selections are complementary methods that offer opportunities for the speedy choice of contrasting parents and derived progenies for hybrid breeding and commercialization. Genomic selection (GS) will shorten the crop breeding cycle by identifying and tracking desirable genotypes and aid the timeous commercialization of market-preferred varieties. The technology, however, has not yet been fully embraced by most public and private breeding programmes, notably in Africa. This review aims to present the importance, current status, challenges and opportunities of GS to accelerate genetic gains for economic traits to speed up the breeding of high-yielding maize varieties. The first section summarizes genomic selection and the contemporary phenotypic selection and phenotyping platforms as a foundation for GS and trait integration in maize. This is followed by highlights on the reported genetic gains and progress through phenotypic selection and GS for grain yield and yield components. Training population development, genetic design and statistical models used in GS in maize breeding are discussed. Lastly, the review summarizes the challenges of GS, including prediction accuracy, and integrates GS with speed breeding, doubled haploid breeding and genome editing technologies to increase breeding efficiency and accelerate cultivar release. The paper will guide breeders in selection and trait introgression using GS to develop cultivars preferred by the marketplace.     

Assessing the genetic diversity of Portuguese maize germplasm using microsatellite markers

A collection of Portuguese maize accessions representing a valuable source of genes for introduction into modern cultivars is stored at the Portuguese Plant Germplasm Bank (Banco Português de Germoplasma Vegetal—BPGV). To assess genetic diversity among inbreds, microsatellite analysis was carried out for 54 inbred lines representing the diversity of Portuguese dent and flint maize germplasm. Fifty American and other European elite inbreds were also analysed for comparison. Fifteen microsatellite loci distributed throughout the maize genome were chosen based on their repeat unit and base composition. A total of 80 alleles were detected with an average allele number of 5.33 per locus. Polymorphism information content (PIC) values and observed genetic distances showed the existence of large variability among inbreds. Cluster analysis indicated that almost all of the inbreds could be distinguished from each other and Portuguese inbreds were present in all clusters formed. These associations were consistent with the known pedigree records of the inbreds, confirming a mixed origin of Portuguese materials. Comparative analysis of microsatellite diversity among groups was established according to important traits for both breeding and line identification. This revealed that, although most of the genetic diversity (>95%) was attributable to differences among inbreds of different groups, the existence of phenotypic differentiation in endosperm colour, kernel type and cob colour could be suggested for grouping. These findings support the joint use of molecular and morphological traits in management of the germplasm collection. In this study, SSR markers proved to be effective to characterise and identify maize inbred lines, and demonstrate associations among them. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic variability,heritability and correlation among agronomic and disease resistance traits in a diversity panel and elite breeding material of spelt wheat

Spelt wheat (Triticum spelta L.) is an old‐world crop that has attracted increased attention since the 1970s accompanied by a constant increase in spelt production. Our objectives were to (i) study the genetic variability and heritability of important agronomic traits and (ii) examine the correlation among these traits for an efficient design of spelt breeding schemes. To this end, we compared a diversity panel of 150 old and new spelt varieties with current elite‐breeding material. Phenotypic data were recorded at multiple locations for yield, plant height, lodging, heading time, number of spikelets, ear snapping and susceptibility to powdery mildew, brown rust and Septoria tritici blotch. We observed highly significant genetic variances for almost all traits in both germplasm sets. Heritability estimates ranged from 0.23 for Septoria tritici blotch to 0.97 for plant height. A significant correlation between yield and plant height of ?0.56 as well as yield and lodging of ?0.39 was determined but no other correlation of yield with any of the examined traits. Thus, pedigree selection with early generation screenings on plant height and lodging can be recommended for further spelt improvement.     

玉米产量及产量相关性状QTL的图谱整合

利用生物信息学方法,借助高密度分子标记遗传图谱IBM2 2008 neighbors,利用图谱映射和元分析的方法,对不同试验中定位的400个玉米产量及产量相关性状QTL进行了图谱整合,构建了玉米产量及产量相关性状QTL的综合图谱和一致性图谱。结果表明,玉米产量及产量相关性状QTL在10条染色体上呈非均匀分布,第1染色体上最多,第10染色体上最少;发掘出96个玉米产量及产量相关性状的“一致性”QTL;关联性较强的产量性状的QTL常集中在相同或相近的座位上。     

玉米“黄金”群体产量等性状轮回选择改良效果评价研究

利用群体改良方法,充分挖掘地方优异种质的遗传潜力是玉米种质改良与创新的一个重要途径。本研究以黄金群5个轮次改良群体为材料,通过1年2点产量比较试验,分析了混合选择和相互半姊妹轮回选择方法对黄金群产量及穗部性状的改良效果。结果表明,两种选择方法对群体产量改良是有效的,随着改良轮次的增加,黄金群的单株产量逐轮提高,平均每轮提高3.78%,其中,混合选择改良的3轮群体平均每轮提高4.27%,相互半姊妹轮回选择的改良群体提高2.07%;虽然群体产量的变异系数从15.43%下降到12.80%,但群体内仍有较丰富的变异。通过改良群体穗部性状比较发现,穗长和行粒数改良效果显著,分别提高14.71%和17.62%,说明它们的提高是群体单株产量提高的主要因素。     

基于SSR的四川花生遗传多样性分析

[目的]研究旨在了解四川花生资源的遗传多样性及表型性状与分子标记的关联分析,为花生分子育种及资源库构建提供理论依据。[方法]鉴定分析57份不同来源花生资源材料的4个农艺性状及4个品质性状,并利用SSR标记研究57份花生材料的遗传多样性,对SSR标记与表型性状进行聚类及关联分析。[结果]表型性状鉴定结果显示花生资源的8个性状中,6个变异较大、多样性较好。67对SSR引物中,有效引物39对,获得多态性条带53条,平均每个引物扩增1.36条,平均Nei"s 基因多样性0.2288、平均Shannon"s 指数0.3695,最远遗传距离为0.51。SSR分子标记聚类分析将57份资源聚为2大类群,GLM分析发现多个与蛋白质含量、株高、含糖量的关联标记。[结论]研究结果表明,四川不同区域间花生遗传多样性较丰富,品种类型单一,聚类及关联分析结果可为四川花生突破性新品种选育的亲本选择提供提供重要参考。     

What is the SMARTest way to breed plants and increase agrobiodiversity?

The evaluation and use of the vast diversity contained in plant genetic resources (PGR) is a main challenge for today’s plant breeding. The use of molecular markers has hugely increased the knowledge about genetic diversity and great hopes are raised about the potential of marker assisted selection [MAS; sometimes also termed SMART breeding (Selection with Markers and Advanced Reproductive Technologies)] to help increasing the use of PGR and maintaining crop genetic diversity. Another approach growing attention has been paid to over the past two decades and which also aims to increase variation in crops is evolutionary and participatory breeding (EPB). In this paper we discuss both the potential of marker-assisted breeding strategies and the potential of EPB breeding to contribute to the maintenance, increase and development of agrobiodiversity. The potentials of molecular markers in the evaluation and use of PGR and their documented contribution to agrobiodiversity are reviewed and results from guided interviews with scientists and breeders are given. Despite tremendous research efforts involving molecular markers, it is still difficult to obtain a clear picture how molecular markers contribute to the use of PGR in plant breeding. Minor and major crops do not benefit to the same degree from recent developments in marker technology. It therefore depends at least in part on economic considerations whether SMART breeding or EPB strategies or both are implemented in the breeding process of a crop. A general decision in favor or against MAS or EPB when breeding for diversity would not yield optimum results.     

Evaluation of strategies to optimize training populations for genomic prediction in oat (Avena sativa)

Genomic selection is a promising breeding methodology that could increase selection accuracy and intensity and reduce generation interval. As the cost of genotyping decreases, it will be important to optimize training populations for costly phenotypic experiments for many complex traits. The aim of this research was to evaluate different optimization strategies, by using historical data from the Norwegian oat breeding programme at Graminor. In this paper, we focus on the optimization criteria: genetic diversity, phenotypic variance and genetic similarity between the training and testing populations. The four training population strategies—prediction core, diversity core, phenotypic selection and random selection—were applied to an oat candidate population of 1124 lines. An independent testing population was used to calculate the mean prediction abilities for the traits days to heading and plant height. Moreover, the strategies were tested in three independent wheat populations. The results showed that prediction core was the most promising strategy to select training populations with high genetic similarity to the testing set, high genetic diversity, and high phenotypic variance, which resulted in higher prediction ability across population sizes and traits.     

西南及四川区试玉米组合遗传多样性分析

采用表型性状分析、SSR标记和系谱分析对186个区试及引种试验玉米组合进行遗传多样性分析。结果表明,各组合间20个表型性状都变异在一个较小的范围内;利用筛选出的60对扩增条带清晰、具明显多态性的SSR引物,共检测到608个等位基因,每对引物检测到3~23个等位基因,平均为10.1个;SSR多态信息量（PIC）分布范围为0.5179~0.9256,平均值为0.7826;186个组合的遗传相似系数变幅在0.6067~0.9162之间,平均值为0.7722,相似系数在0.7000以上的组合有16 499对,占96.9%,供试材料分为10类,且88.2%的组合集中在第4、8、10类;51个系谱清楚的组合中有36个（占70.58%）与美国的PN种质有密切关系。以上结果均表明,供试组合相似程度较高,遗传差异较小,遗传基础相对单一,进一步拓展玉米种质遗传基础仍然显得十分必要。     

玉米抗穗粒腐病QTL定位

用已构建的包括88个AFLP标记和151个SSR标记的遗传图谱和230个F₂植株用于抗病QTL定位研究,在四川雅安、绵阳对F2株系进行抗病性鉴定,采用复合区间定位法进行抗病QTL检测。在雅安检测到位于第2、3、4、6和9染色体上的抗病QTL 6个,解释表型变异的8.3%~25.7%;在绵阳检测到位于第1、6、7和9染色体上的抗病QTL 4个,解释表型变异的11.3%~26.4%。在10个抗病QTL中,位于第6和第9染色体上的2个同时在两点被检测到,贡献率均超过15%,表明玉米穗粒腐病确实存在遗传抗病性。利用2个环境抗病指数的平均值进行抗性QTL检测,共检测到位于第1、6和7连锁群上的3个抗性QTL,单个QTL的贡献率在8.9%~17.2%之间。结果有助于了解玉米穗粒腐病的抗性机制,并为分子标记辅助选择提供理论支撑。