Genomic Prediction of Testcross Performance in Canola (Brassica napus)

Genomic selection (GS) is a modern breeding approach where genome-wide single-nucleotide polymorphism (SNP) marker profiles are simultaneously used to estimate performance of untested genotypes. In this study, the potential of genomic selection methods to predict testcross performance for hybrid canola breeding was applied for various agronomic traits based on genome-wide marker profiles. A total of 475 genetically diverse spring-type canola pollinator lines were genotyped at 24,403 single-copy, genome-wide SNP loci. In parallel, the 950 F1 testcross combinations between the pollinators and two representative testers were evaluated for a number of important agronomic traits including seedling emergence, days to flowering, lodging, oil yield and seed yield along with essential seed quality characters including seed oil content and seed glucosinolate content. A ridge-regression best linear unbiased prediction (RR-BLUP) model was applied in combination with 500 cross-validations for each trait to predict testcross performance, both across the whole population as well as within individual subpopulations or clusters, based solely on SNP profiles. Subpopulations were determined using multidimensional scaling and K-means clustering. Genomic prediction accuracy across the whole population was highest for seed oil content (0.81) followed by oil yield (0.75) and lowest for seedling emergence (0.29). For seed yieId, seed glucosinolate, lodging resistance and days to onset of flowering (DTF), prediction accuracies were 0.45, 0.61, 0.39 and 0.56, respectively. Prediction accuracies could be increased for some traits by treating subpopulations separately; a strategy which only led to moderate improvements for some traits with low heritability, like seedling emergence. No useful or consistent increase in accuracy was obtained by inclusion of a population substructure covariate in the model. Testcross performance prediction using genome-wide SNP markers shows considerable potential for pre-selection of promising hybrid combinations prior to resource-intensive field testing over multiple locations and years.     

Inheritance of seed yield and quality traits in peas (Pisum sativum L.)

Summary A half diallel analysis involving nine cultivars showed that additive as well as non-additive gene effects were important for the inheritance of seed yield per plant, 100-seed weights, protein content and potassium per cent. For remaining traits non-additive genetic components were important. Overdominance was observed for all traits except for 100-seed weight, which expressed partial dominance. Parents PMR-T10, EC21857, EC109182, T163 and EC109189 were good general combiners for seed yield, seed weight and quality traits. In general there was a good relationship between per se performance and the gca effects of the parents for all traits. Cross combinations such as LMR8 x EC109182,LMR8 x PMR-T10,LMR8 x EC21857,PMRT10 x EC21857 and P23 x EC21857 were found promising. The seed yield was positively correlated with other quality traits. Protein had a positive correlation with methionine and phosphorus. All the values of correlation co-efficients were non-significant except for yield with potassium, 100-seed weight and protein with methionine, indicating that yield and quality attributes can be improved simultaneously by simple selection procedures.     

Seedling development in a Brassica napus diversity set and its relationship to agronomic performance

Brassica napus L. is the leading European oilseed crop and has therefore a high economical importance. The objectives of our study were to examine (1) the patterns of phenotypic diversity in a species-wide B. napus germplasm set of 518 inbreds with respect to various seedling development, agronomic, and seed quality traits as well as (2) the interrelationship of the examined traits and their use in selection on correlated traits. The B. napus germplasm set was evaluated in greenhouse and field trials for several seedling development, agronomic, and seed quality traits. The traits were highly correlated within the individual trait categories and moderately correlated between the different trait categories. We observed differences in phenotypic diversity among the examined eight germplasm types. The reduction of phenotypic diversity was on average more pronounced for the seedling development traits than for the agronomic and seed quality traits, suggesting that plant breeders need to introgress new genetic variation with respect to the former.     

Combining ability in the F1 and F2 generations of diallel cross in hexaploid wheat (Triticum aestivum L. em. Thell)

The F(1) and F(2) progenies of a ten-parent diallel cross (excluding reciprocals) of hexaploid wheat (Triticum aestivum L. em. Thell) were analyzed for combining ability for quantitative and quality traits. The results indicated significant differences among the parents for general combining ability (gca) and crosses for specific combining ability (sca) for all the characters studied. The gca and sca components of variance were significant for all the traits. However, the gca component of variance was predominant indicating the predominance of additive gene effects for the traits studied. Among the parents Durgapura 65, HD 2285, Lok-1, Raj 1972 and HD 2329 were the best general combiners for grain yield and average to high combiners for tillers per plant, grain yield per spike, grains per spike and 1000-grain weight. The best specific crosses for grain yield were Sonalika x WH 157, HD 2428 x Durgapura 65, Durgapura 65 x Sonalika, HD 2428 x Lok-1 and CPAN 3004 x Raj 1972. The parent Raj 1972, Lok-1 and HD 2285 were the best general combiners for grain yield and protein content, however, Raj 3077 was the best general combiner for protein content. The most suitable specific crosses for protein content were HD 2329 x HD 2285, HD 2428 x Raj 1972 and CPAN 3004 x WH 157. Most of the specific crosses for grain yield as well as protein content involved high x average, average x average and average x poor general combiners. To ensure further increase in grain yield along with high protein, combinations of desirable yield components is advocated. Inclusion of F(1) hybrids showing high sca and having parents with good gca, into multiple crosses and/or bi-parental mating, or diallel selective mating could prove a worthwhile approach for further improvement of grain yield in bread wheat.     

Diallel analysis to predict heterosis and combining ability for grain yield,yield components and bread-making quality in bread wheat (T. aestivum)

Combining ability for grain yield, yield components, and several agronomic and qualitative traits, was studied in a seven-parent diallel cross. The 21 F₁ hybrids and the seven parental cultivars were grown in replicated plot trials sown at normal seed density in three locations in the years 1992 and 1993. The effects of general combining ability (gca) were highly significant for all the traits measured with the exception of seeds per spikelet, while the specific combining ability (sca) effects were statistically significant for grain yield, plant height, heading time, for all the yield components, and for the Chopin alveographic parameters P and P/L ratio. For the majority of the traits measured gca was greater than sca. Standard heterosis (sh) for grain yield, i.e., the superiority of the hybrids over the best pure line cultivar(cv Eridano), was only 3.3%, confirming previous finding which indicate sh effects in the range of 10%. The most interesting hybrid derived from the cross Maestra x Golia revealed a yield level approaching that of the highest yielding cv Eridano but appeared more interesting because of its reduced plant height and superior bread-making quality, signifying a selling price 30% higher. It was concluded, therefore, that the first generation of hybrids, likely to appear on the market in the next few years, will be characterized by a yield potential only slightly superior to that of the best standard cvs but associated with other desirable traits, such as bread-making quality.     

籼型黑米粒形性状的遗传效应及其与矿质元素含量的遗传相关性

采用禾谷类作物种子数量性状的遗传模型,分析了灿型黑米稻品种双列杂交F1和F2种子的粒重,粒长,粒宽和粒长／粒宽等粒形性状的遗传效应及其与米粒中矿质元素Fe,Zn,Mn和P含量的遗传相关性,结果表明：4种粒形性状同时受制于种子直接遗传效应,母体效应和细胞质作用影响,其中种子直接遗传效应比母体效应和细胞质效应的作用更大,且种子直接遗传效应以加性效应占主导,粒重,粒宽和粒长／粒宽的种子直接遗传率较高,杂种早代单粒选择效果较好,粒长的种子直接遗传率和母体遗传率均属中等,较高世代的杂种进行单株选择和单粒选择均有一定效果,4种粒形性状与其米粒中矿质元素Fe,Zn,Mn和P含量表现较强的种子直接加性相关,直接显性相关,细胞质相关,母体加性相关和母体显性相关,在特种稻育种实践中,可以通过粒形性的间接选择,达到改良其矿质元素含量等营养品质性状的目标。     

Genetic analysis of agronomic characters in chickpea

Summary Twenty-eight diallel trials over 8 years and two locations were analysed to estimate genetic variances for agronomic characters of chickpea (Cicer arietinum L.). The data were analysed according to Method 4 and Model I of Griffing (1956). Days to flowering, plant height, and seed size were found to be predominantly under additive inheritance and were highly predictable. Both additive and non-additive genetic components were important for seed yield, number of branches, pods per plant, and seeds per pod. Although both general combining ability (gca) and specific combining ability (sca) varied significantly with generation, components of gca mean squares were invariably much larger than gca x generation interaction components, indicating that either the F₁ or the F₂ generation can be used to estimate the gca components effectively. Combined diallel analysis of F₂s over locations revealed the importance of combining ability x location interactions and emphasized the need for testing over more than one location for the precise estimation of combining ability. The implications of these findings and those reported earlier in the literature on the breeding strategies/methods for the genetic improvement of agronomic characters in chickpea are discussed.ICRISAT journal article no. 1199     

中国17个优良玉米自交系的分子标记杂合性及其与杂交种性状的关系研究

在玉米单交种育种中 ,鉴定高产杂交种和具有优良特性的自交系是一个重要的问题。研究以 1 7个优良玉米自交系为亲本 ,按照双列杂交配组合 ,利用 RAPD技术分析了 1 7个自交系的多态性以及 RAPD标记与 9个重要农艺性状 (包括产量 )的关系。基于 RAPD标记计算的相似系数聚类将 1 7个自交系分为 5个类群 ,经分析与系谱亲缘关系基本一致。杂交种性状及其特殊配合力与亲本间的遗传距离是高度相关的 ,与聚类前比较 ,聚类后平均遗传距离与平均产量、平均特殊配合力的相关系数显著提高 ,类间平均产量高于类内平均产量。RAPD技术可揭示优良玉米自交系的系谱亲缘关系 ,将自交系划分成不同的类群 ,从而为选择类间自交系杂交 ,进行亲本选配和分子标记辅助育种提供一种方法。     

Exploring the natural variation for seedling traits and their link with seed dimensions in tomato

The success of germination, growth and final yield of every crop depends to a large extent on the quality of the seeds used to grow the crop. Seed quality is defined as the viability and vigor attribute of a seed that enables the emergence and establishment of normal seedlings under a wide range of environments. We attempt to dissect the mechanisms involved in the acquisition of seed quality, through a combined approach of physiology and genetics. To achieve this goal we explored the genetic variation found in a RIL population of Solanum lycopersicum (cv. Moneymaker) x Solanum pimpinellifolium through extensive phenotyping of seed and seedling traits under both normal and nutrient stress conditions and root system architecture (RSA) traits under optimal conditions. We have identified 62 major QTLs on 21 different positions for seed, seedling and RSA traits in this population. We identified QTLs that were common across both conditions, as well as specific to stress conditions. Most of the QTLs identified for seedling traits co-located with seed size and seed weight QTLs and the positive alleles were mostly contributed by the S. lycopersicum parent. Co-location of QTLs for different traits might suggest that the same locus has pleiotropic effects on multiple traits due to a common mechanistic basis. We show that seed weight has a strong effect on seedling vigor and these results are of great importance for the isolation of the corresponding genes and elucidation of the underlying mechanisms.     

Combining ability analysis of beta-Carotene,total carotenoids and other grain characteristics in pearl millet

Summary Combining ability studies with respect to grain quality characteristics viz., beta-Carotene, total carotenoids, protein content, 250-grain weight, grain hardness and grain yield were carried out from a 13x13 diallel cross set in pearl millet [Pennisetum typhoides (Burm S&H)].The parents versus hybrids comparison indicated significant heterosis for all the traits under study. In general the hybrids having higher grain yield had bold hard grains with more carotene but low protein content, although a few hybrids combined high yield with an average protein percentage. The relative proportions of the general and specific combining ability variances indicated predominance of non-additive genetic variance with respect to all the traits. The per se performance of parents provided a fairly good indication of their combining ability in most cases. Parents possessing desirable grain quality characteristics were identified. Breeding implications are discussed.Part of the Ph.D. dissertation submitted to the Punjab Agricultural University by the senior author in partial fulfilment of the requirements for the degree     

Seed mucilage improves seedling emergence of a sand desert shrub

The success of seedling establishment of desert plants is determined by seedling emergence response to an unpredictable precipitation regime. Sand burial is a crucial and frequent environmental stress that impacts seedling establishment on sand dunes. However, little is known about the ecological role of seed mucilage in seedling emergence in arid sandy environments. We hypothesized that seed mucilage enhances seedling emergence in a low precipitation regime and under conditions of sand burial. In a greenhouse experiment, two types of Artemisia sphaerocephala achenes (intact and demucilaged) were exposed to different combinations of burial depth (0, 5, 10, 20, 40 and 60 mm) and irrigation regimes (low, medium and high, which simulated the precipitation amount and frequency in May, June and July in the natural habitat, respectively). Seedling emergence increased with increasing irrigation. It was highest at 5 mm sand burial depth and ceased at burial depths greater than 20 mm in all irrigation regimes. Mucilage significantly enhanced seedling emergence at 0, 5 and 10 mm burial depths in low irrigation, at 0 and 5 mm burial depths in medium irrigation and at 0 and 10 mm burial depths in high irrigation. Seed mucilage also reduced seedling mortality at the shallow sand burial depths. Moreover, mucilage significantly affected seedling emergence time and quiescence and dormancy percentages. Our findings suggest that seed mucilage plays an ecologically important role in successful seedling establishment of A. sphaerocephala by improving seedling emergence and reducing seedling mortality in stressful habitats of the sandy desert environment.     

繁殖世代对水稻植株农艺性状及稻米品质的影响研究

以国家长期库躬存种质为对照,选择在生产上一直种植的同一品种为高繁殖世代材料,一起进行田间种植以了解两者之间在田间出苗率、生育期、植株农艺性状及稻米品质上是否存在差异。结果表明,在6个供试粳稻品种中,有5个品种的高繁殖世代种质,其稻米垩白品质出现了退化现象,而其他稻米品质特性没有出现明显的变化。来自库存的种质,其每穗粒数都比一直在生产上种植的种质少,这可能与母本长时间低温贮藏有关。此外,来自库存的种质,其田间出苗率也相对较低。     

Inheritance of emergence time and seedling growth at low temperatures in four lines of maize

Summary The improvement of rate of seedling emergence and early seedling growth of maize (Zea mays L.) under cool conditions has been an objective of breeding programs in cool regions for many years. To study inheritance of emergence time, and to determine if differences in emergence time were due to differences in seedling growth, F₁, F₂ and backcross generations of a diallel cross of two rapidly emerging lines from CIMMYT Pool 5, 5-113 and 5-154, and two elite Corn Belt Dent lines, A619 and A632, were grown in controlled environment rooms at low temperatures.The lines from Pool 5 emerged significantly faster than A619 and A632 over a range of low temperature conditions. This difference occurred both when the lines themselves were tested and when the lines were tested as male and female parents in crosses. The Pool 5 lines converted a higher proportion of their original seed to new root and shoot tissue than did A619 and A632, indicating that they had a faster seedling growth rate. Primarily this was due to a faster loss of seed reserve, rather than a more efficient conversion process.A significant difference occurred between A619 and A632 for emergence time, but this was not due to a difference in seedling growth rate.Reciprocal differences occurred only in the F₁ generation in crosses involving A619, and then marked effects could be attributed to the male parent. Reciprocal differences tended to disappear in the F₂. This suggested that the genotype of the embryo and endosperm was of much greater importance than the genotype of the maternal parent in determining differences of time to emergence and seedling growth.Mid-parent heterosis occurred for time to emergence and seed loss, a measure of mean rate of utilization of seed reserve, in all crosses. High parent heterosis occurred in several crosses for these traits. High parent heterosis occurred in all crosses for efficiency of utilization of seed reserve.A generation means analysis indicated that both additive and dominance effects were present for rate of seedling growth in crosses between A632 and the Pool 5 lines.     

不同遗传背景下杂交籼稻功能叶与产量构成因素的相关性

为明确水稻功能叶与产量构成因素间的相关性,以不同遗传背景下籼稻的10个不育系和16个恢复系为亲本,按照NCII设计配制两套双列杂交组合,对水稻12个功能叶性状与8个产量性状构成因素进行了相关分析,结果表明：3片功能叶叶长与叶面积、剑叶宽、倒2叶宽等性状之间均存在极显著正相关,功能叶夹角之间也存在极显著正相关,但不同遗传背景对夹角性状与9个形态性状之间的相关性则存在明显差异,在第1套组合中,其相关系数均为负值,且相关均不显著;而第2套组合则相反。8个产量构成因素中,单株穗数与平均穗长、着粒密度、穗实粒数以及穗着粒数之间存在极显著负相关,平均穗长与穗着粒数、结实率与单株产量呈显著或极显著正相关,遗传背景对产量组成上有较大影响,在第1套组合中单株产量主要由结实率、单株穗数以及穗实粒数等性状决定,而在第2套中则主要由穗实粒数和结实率等性状决定。在功能叶与产量构成因素的相关中,叶长、叶面积、剑叶宽、倒2叶宽与着粒密度、穗实粒数以及穗着粒教等3个性状之间存在显著或极显著正相关。12个水稻功能叶性状与8个产量构成因素之间的主成分分析表明,在不同的遗传背景下,产量构成因素均主要受叶面积和叶夹角影响,两种不同遗传背景中其累积贡献率分别为69．8％和84．0％。     

Seed mass versus seedling performance in Scots pine: a maternally dependent trait

It is generally accepted that larger seeds give rise to seedlings with better performance. On the other hand, the size that a seed reaches is genetically determined by at least two different traits ; the genetic variability of the developing embryo and the genetic variability of the maternal plant. Thus, the relative contributions of these two traits affect seedling performance by influencing seed size. In this paper, I investigate the effect of seed size on seedling performance in the Scots pine ( Pinus sylvestris ). From eight maternal plants, 50 seeds were planted in each of two soil types (800 seeds in total), and seedling performance was monitored for 1 yr. Seed mass proved to be highly constant within maternal plants. Soil type influenced emergence and survival; however, the effect of soil type differed depending on maternal origin. Seed mass was positively correlated with seedling emergence, although this relationship was not found for seedling survival or date of emergence. The initial growth of the shoot was also positively correlated with seed mass. However, after one growing season, seed mass had no effect on seedling performance, which depended exclusively on maternal origin. Nevertheless, the mean mass of seeds produced by plants was positively correlated with mean values of growth parameters. Thus, first-year seedling performance seems to be a maternal trait indirectly associated with seed size.     

Estimation of genetic parameters in barley (Hordeum vulgare L.)

Summary Four exotic and four indigenous strains of barley were used for making diallel crosses. The sets of parents and crosses making full, half and quarter diallel were analysed in a randomized block design for plant height, number of effective tillers, ear length, grain yield per plant, 100 grain weight and number of grains per ear.The three alternatives of diallel were similar with respect to the estimates of degree of dominance, general combining ability and specific combining ability, indicating that all these three methods of diallel were equally efficient. However, as the number of entries are minimum in quarter diallel, it would be economical in terms of cost, time and labour to estimate genetic parameters by this method. Average degree of dominance was found in the range of overdominance. The ranking of parents on the basis of their array mean was similar to the ranking based on gca effects. Similarly, the ranking of crosses on the basis of per se performance was similar to the ranking based on sca effects. This suggests that the selection of best general combiner or best cross combinations may be easier and more effective through array mean for per se performance rather than through high gca and sea effects, respectively. From among 56 crosses, IB-226 X X C-164 was the one which showed superiority for maximum number of characters followed by AB-12/59 X PTS-57. High sea effect for plant height, ear length, grain yield, 100 grain weight and number of grains per ear was the result of cross between parents having high X low general combining ability, indicating additive X dominance type of gene interaction. For number of effective tillers, high sca was produced by low x low general combiners, indicating dominance x dominance gene interaction.Part of a Ph. D. thesis submitted by senior author to Haryana Agricultural University, Hissar.     

Yield stability in Coffea canephora from diallel mating designs monitored for 14 years

The genetic parameters of several agronomic traits were estimated in Coffea canephora in a triangular diallel with six parents and in a partial diallel with 18 parents. The yield data came from harvests obtained over 14 years divided into an initial 6-year cycle, a second cycle of 5 years after cutting back and a third cycle of 3 years after topping. Risk incidence was also observed over several years. The general combining abilities (GCA) were the principal sources of variation for the various traits considered. Parents derived from the Yangambi selections (Democratic Republic of Congo) proved to be best for yields in the three cropping cycles. The rank correlations between the GCA of the various traits indicated that first-cycle production was still not enough to predict the GCA for yield over 14 years. Susceptibility to leaf anthracnose and to drought could lead to modifications in successive classifications, with a more significant impact on production during the first cycle. The differences in susceptibility to Coffee Berry Borers had an impact on yield, which increased in line with coffee tree age. There was a rather good relation between inherent values and values in parent combinations and it was thus possible to choose parents on their own performance.     

Genetic diversity for RFLPs in European maize inbreds

Summary Restriction fragment length polymorphisms (RFLPs) have been proposed for the prediction of the yield potential of hybrids and the assignment of inbreds to heterotic groups. Such use was investigated in 66 diallel crosses among 6 flint and 6 dent inbreds from European maize (Zea mays L.) germ plasm. Inbreds and hybrids were evaluated for seven forage traits in four environments in the Federal Republic of Germany. Midparent heterosis (MPH) and specific combining ability (SCA) were calculated. Genetic distances (GD) between lines were calculated from RFLP data of 194 clone-enzyme combinations. GDs were greater for flint x dent than for flint x flint and dent x dent line combinations. Cluster analysis based on GDs showed separate groupings of flint and dent lines and agreed with pedigree information, except for 1 inbred. GDs of all line combinations in the diallel were partitioned into general (GGD) and specific (SGD) genetic distances; GGD explained approximately 20% of the variation among GD values. For the 62 diallel crosses (excluding 4 crosses of highly related lines), correlations of GD with F₁ performance, MPH, and SCA for dry matter yield (DMY) of stover, ear, and forage were positive but mostly of moderate size (0.09r0.60) compared with the higher correlations (0.39r0.77) of SGD with these traits. When separate calculations were performed for various subsets, correlations of GD and SGD with DMY traits were generally small (r<0.47) for the 36 flint x dent crosses, significantly positive (r<0.53) for the 14 flint x flint crosses, and inconclusive for the 12 dent x dent crosses because of the lack of significant genotypic variation. Results indicated that RFLPs can be used for assigning inbreds to heterotic groups. RFLP-based genetic distance measures seem to be useful for predicting forage yield of (1) crosses between lines from the same germ plasm group or (2) crosses including line combinations from the same as well as different heterotic groups. However, they are not indicative of the hybrid forage yield of crosses between unrelated lines from genetically divergent heterotic groups.     

利用普通野生稻褐飞虱抗性改良水稻恢复系的研究

褐飞虱是我国水稻主要害虫之一,挖掘和利用稻飞虱抗性基因,选育抗稻飞虱的水稻品种是目前防治褐飞虱最科学、安全的一种措施。本研究利用具有高抗褐飞虱显性基因的抗源材料HS204作为抗源供体,以恢复系明恢65、582、MR等作为轮回亲本,通过回交,苗期群体鉴定和成株期农艺性状选择,成功地将高抗褐飞虱基因转育到轮回亲本中,获得45份抗性纯合株系,同时其配合力、米质等其他农艺性状也得到了相应改善。