Virtual modeling based on deep phenotyping provides complementary data to field experiments to predict plant emergence in oilseed rape genotypes

Breeding oilseed rape for oil and protein contents may have led to differences in seedling emergence in genotypes. New opportunities for deep automated phenotyping of germination and seedling growth are being developed on phenotyping platforms. Our aim was to demonstrate that using these data to parameterize a crop emergence model complements field experiments for the evaluation of differences among genotypes. Five genotypes, chosen in a diverse set of winter oilseed rape for their different germination speeds, were phenotyped for germination at different temperatures and water potentials as well as for radicle and hypocotyl growth. These data were used as parameters to run the SIMPLE crop emergence model over a period of 27 years (1985–2012), at two locations, one in France and one in Germany, and at four sowing dates. Field experiments were performed in 2012, 2013 and 2014, and the emergence of the five genotypes was measured at early and late sowing dates. First, model predictions were compared with observed field emergence in the French sowing trials in 2014. The model proved to be rather good at predicting the emergence of the genotypes. Then, for the simulation study, the model extended the observed differences between locations and sowing dates over a greater number of years. The model also identified the main reasons for non-emerging seedlings and their frequencies in the simulated sowings. Differences between the five genotypes were on average very small, but complex interactions appeared that led to bigger differences under certain sowing conditions. This study demonstrates that combining deep phenotyping with crop models in simulation studies paves the way for more precise and detailed evaluation of genotypes.     

Inheritance and expression of transgenes in T2 and T3 generations of Lotus corniculatus transformed using Agrobacterium tumefaciens

The inheritance and expression of the reporter gene uidA, encoding β-glucuronidase (GUS), was previously analysed in the T₁ generation of 25 independent transformed lines of Lotus corniculatus cv. Leo. In the work reported here, GUS activity in various tissues of seven of these lines was tested in the T₂ generation. Four representative lines were chosen for more detailed study in the T₃ generation. Lines 25 and 38 had multiple, independently segregating transgene inserts; lines 24 and 39 appeared to transmit one segregating transgene insert to their T₁ progeny, although transgene expression was low and was detected in fewer seedlings than expected in line 39. The uidA gene was inherited and expressed in seedlings of T₁, T₂ and T₃ generations of all four lines. In all lines, transgene expression varied between tissues, with more embryos than seedlings having detectable GUS activity. Studies in the T₂ generation showed that use of transgenic plants as female or male parents altered the frequency of expression of the transgene in progeny. By contrast, in the T₃ generation the use of transgenic plants as female or male parents did not effect either frequency of transmission, or expression of the transgene, in any of the four lines. Transgene inheritance was also similar among individual pods within flower heads and between individual flower heads. This revised version was published online in July 2006 with corrections to the Cover Date.     

Using tube rhizotrons to measure variation in depth penetration rate among modern North-European winter wheat (Triticum aestivum L.) cultivars

Deeper plant root systems are desired for improved water and nitrogen uptake in leaching environments. However, phenotyping for deep roots requires methods that enable plants to develop deep roots under realistic conditions. Winter cereals raise further complications as early growth occurs under low light and temperature during autumn and winter—conditions not met in standard glasshouse facilities. This study used tube rhizotrons of 2 m length, positioned outdoor under a rainout shelter to screen for depth penetration rates (DPR) of roots. Rooting depths of 1 to 1.5 m were achieved with 23 widely grown North European winter wheat cultivars in two autumn/winter and two summer experiments and nine of the cultivars were represented in two or more experiments. Heritability of DPR of roots was only consistent in autumn/winter experiments (27 %) signifying the importance of phenotyping in relevant seasons and environments. Depth penetration rate of roots varied significantly within the tested cultivars, from 1.39 (±0.35) mm °C^?1 day^?1 for cv. Tuareg to 2.07 (±0.34) mm °C^?1 day^?1, for cv. Mercedes. This study documented consistent differences of DPR among North-European winter wheat cultivars in long tube rhizotrons under semi-natural conditions, which may form part of future phenotyping facilities for deep rooting traits.     

Variation in seed proteins from mutagen-treated cultivars and selected lines of Vigna unguiculata L. Walp

The storage protein profiles of the seeds of two IITA cowpea cultivars (‘IT84E–124’ and ‘Vita 7’) exposed to three mutagens—sodium azide (NaN₃), ethyl methane sulphonate (EMS) and ⁶⁰Co gamma rays—and those of 18 selected M₃ lines were investigated by sodium dodecyl sulphate (SDS)-polyacrylamide gel electrophoresis (PAGE). The total seed protein, globulin and albumin fractions showed differences in number and intensity of subunit bands, but the least differences were found in the albumin fraction. Both high and low molecular weight bands were observed, the highest being 94.5 kDa and the lowest 12.0 kDa.‘Vita T showed less variability compared with ‘IT84E–124’, as indicated by the relative similarity indices (S.I.) of the two cultivars. The lowest S.I. of 0.200 was found among ‘IT84E–124’ lines while the lowest S.I. among ‘Vita T lines was 0.4706. A number of lines with particular traits were found to be characterized by the presence of specific polypeptide bands. This study demonstrates that induced mutation could create additional variability to supplement existing germplasm and that SDS-PAGE is a useful tool for discriminating and estimating genetic similarities among selections.     

Phenotypic evaluation of floral and flowering traits with relevance for hybrid breeding in wheat (Triticum aestivum L.)

Hybrid breeding is a promising approach to increase the yield potential in wheat (Triticum aestivum L.). The profitability of wheat hybrids highly depends on a cost‐efficient system for hybrid seed production for which an adequate outcrossing in the male pool is of utmost importance. Employing a set of 51 elite winter wheat lines, we developed and evaluated phenotyping methods for floral and flowering traits with relevance for improved cross‐pollination. We observed significant genotypic variances and high heritabilities for most traits, including important traits like pollen mass and anther extrusion. Our results suggest the utility of the developed phenotyping approaches for applied plant breeding and the potential of the traits to assist in the design of the male ideotype for increased cross‐fertilization.     

Assessing genetic variation of maize (Zea mays) root DNA density under contrasting water supply

Optimizing root systems is one crucial point in drought tolerance breeding of plants. Introducing root-related traits to breeding programmes is time-consuming and laborious. Most of the commonly used methods are not suitable to be applied in a larger amount of plants. Here we present a study applying a DNA-based root phenotyping method (root DNA density; RDD) for phenotyping the root system of maize. Twenty-one maize inbred lines were investigated in a rain-out shelter experiment and 19 maize inbred lines in a greenhouse experiment under well-watered and drought conditions. Beside other commonly used root traits, agronomic traits of the plants were recorded and compared to RDD. Within root traits, RDD showed high significant genotypic variation and the highest repeatabilities of up to 72.4%. In contrast to most agronomic traits, repeatabilities increased under drought conditions. Values showed also good correlations between rain-out shelter and greenhouse trial, indicating the potential of this method for obtaining comparable results across different environments.     

Screening for low grain cadmium phenotypes in sunflower, durum wheat and flax

Cadmium (Cd) level in nonoilseed sunflower (Helianthus annuus L.), flax (Linum usitatissimum L.), and durum wheat (Triticum turgidum L. var. durum) grown on uncontaminated, alkaline soils has exceeded limits established in Northern Europe. Separate field experiments were conducted to investigate variability of grain Cd levels among sunflower, durum wheat and flax germplasm, and to seek an efficient screening method for future breeding. There were large variations in leaf Cd concentration among 200 sunflower lines. These lines performed more consistently for Cd uptake at the R5 stage than at the V8 stage across 4 locations with markedly differing soils. Cd concentration in V8 leaves was not related to Cd in grain. The positive correlation between R5 leaf Cd and kernel Cd level was obtained from nonoilseed hybrid (Sigco 954) (R²; = 0.74**), and 200 lines (R² = 0.44**) tested over 4 locations in 2 field trials, respectively. This indicates that an efficient and low cost screening method can be developed for genotype selection, but plants must be grown to the R5 stage. A preliminary evaluation of 30 durum wheat and 74 flax lines indicated large variations in grain Cd level of durum wheat and flax. Grain Cd concentration ranged from 0.11 to 0.34 mg Cd kg^-1 DW for durum wheat, and 0.14 to 1.37 mg Cd kg^-1 DW for flax, respectively. This variability indicates that breeding for low grain Cd in durum wheat and flax should be feasible. This revised version was published online in July 2006 with corrections to the Cover Date.     

Physiological attributes associated with yield and stability in selected lines of a durum wheat population

Further increasing yield potential remains one of the main objectives of wheat breeding, even in stressful environments. In general, past genetic gains were associated with increases in harvest index, and future gains should be related to greater biomass. Identifying genetic sources for such improvement may be relevant. Researchers of TRITIMED identified DH lines of durum wheat apparently possessing not only high yield potential but also good yield stability. We aimed to determine physiological attributes responsible for yield and stability among a set of genotypes derived from two parents (Cham 1 and Lahn) and four of the most promising lines of the DH population (2401, 2408, 2410, 2517). Seven field trials were carried out within the Mediterranean agricultural region of the Ebro Valley, under a wide range of conditions (ca 2–10 mg ha⁻¹). In four of these experiments, sub-plots were included with source-sink manipulations imposed after anthesis. Cham 1, a cultivar known for high yields in semi-arid conditions, showed the highest yield potential. Although it showed less yield stability than Lahn, even under the lowest yielding conditions its yield was not significantly lower than that of Lahn. RILs 2408, 2410, 2004 and 2517 slightly outyielded Lahn in high-yielding conditions, but under poorer environments they tended to yield less. Interestingly, yield differences were closely related to their biomass rather than harvest index. Thus yield differences relating to the number of grains per m² were due to differences in spike dry matter at anthesis, reflecting in part genotypic differences in crop growth from jointing to anthesis. In general grain weight did not respond to spike trimming after anthesis, although in two experiments the grain weight of Cham 1 did so. Thus, even the highest-yielding cultivar possessed grains that overall seemed more limited by its constitutive capacity to grow than by the availability of resources to reach this capacity (though occasionally they may be co-limited). Overall, the most interesting feature was the empirical evidence that improvement of biomass within elite material is a worthwhile objective.     

Field evaluation of transgenic Brassica napus lines carrying a seed-specific chimeric 2S albumin gene

The agronomic performance of transgenic Brassica napus lines carrying chimeric 2S albumin seed protein genes was studied under field conditions. A total of 37 transgenic lines were compared to non-transformed lines. Plant development, morphological characteristics, yield parameters and seed composition were considered. Only a few transgenic lines differed from the control, and then only for particular parameters: four lines had altered leaf morphology, two differed in germination efficiency, one differed in yield, and three differed in some parameters of seed composition. These differences were not correlated with the presence or expression of the transgene and, thus, were more probably linked to cell- or tissue-culture effects, or to residual variation present in cv. ‘Drakkar’. A statistical interaction between variations in a limited number of seed composition parameters and cell haploid culture was observed. While the expression of the chimeric 2S albumin gene was not as high as hoped, this study demonstrates that transgenic lines can be isolated in which the intrinsic morphological and agronomic properties of the original lines are maintained.     

Genetics,genomics and breeding of groundnut (Arachis hypogaea L.)

Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker‐assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.     

QTL analysis for thousand-grain weight under terminal drought stress in bread wheat (<Emphasis Type="Italic">Triticum</Emphasis><Emphasis Type="Italic">aestivum</Emphasis> L.)

Grain yield under post-anthesis drought stress is one of the most complex traits, which is inherited quantitatively. The present study was conducted to identify genes determining post-anthesis drought stress tolerance in bread wheat through Quantitative Trait Loci (QTLs) analysis. Two cultivated bread wheat accessions were selected as parental lines. Population phenotyping was carried out on 133 F_2:3 families. Two field experiments and two experiments in the greenhouse were conducted at IPK-Gatersleben, Germany with control and post-anthesis stress conditions in each experiment. Thousand-grain weight was recorded as the main wheat yield component, which is reduced by post-anthesis drought stress. Chemical desiccation was applied in three experiments as simulator of post-anthesis drought stress whereas water stress was applied in one greenhouse experiment. Analysis of variance showed significant differences among the F_2:3 families. The molecular genetic linkage map including 293 marker loci associated to 19 wheat chromosomes was applied for QTL analysis. The present study revealed four and six QTLs for thousand-grain weight under control and stress conditions, respectively. Only one QTL on chromosome 4BL was common for both conditions. Five QTLs on chromosomes 1AL, 4AL, 7AS, and 7DS were found to be specific to the stress condition. Both parents contributed alleles for drought tolerance. Taking the known reciprocal translocation of chromosomes 4AL/7BS into account, the importance of the short arms of homoeologous group 7 is confirmed for drought stress.     

Comparative seed yield performance of high-by-high and low-by-high crosses in flax *

Successful identification of a desirable segregant depends partly on the parents chosen to make the crosses. This experiment was conducted to compare performance and genetic variability for seed yield, yield components, agronomic traits and harvest index of lines derived from low- and high-yielding flax (Linum usitatissimum L.) crosses, and to identify important yield components for flax seed yield improvement. The lines chosen as high yielding parents for this experiment were‘Linott’and 'Summit; and the low yielding parents were‘Grant’and Ci2395. The high-yielding lines produced significantly more seeds per boll and had a higher harvest index than the low-yielding lines. Evaluation of 161 F_2:6 lines from four crosses among these lines showed that the greatest genetic variability, highest cross average, and highest F₆ line seed yield occurred in the low x high cross,‘Grant’x‘Linott’. All low X high crosses exhibited higher genetic variances for seed yield than the high x high crosses. The high x high cross 'Summit’x‘Linott’had low genetic variance for seed yield. Number of bolls per area was determined by linear regression, path coefficient analysis, and stepwise multiple regression analysis to be the most important component of seed yield. This study showed that hybridization of low and high-yielding flax lines may be useful to increase genetic variability and obtain high-yielding flax lines.     

A heuristic method of searching for interesting markers in terms of quantitative traits

Selection of parental lines is important in plant breeding programmes. Marker-assisted selection is an alternative to classical selection methods, which are expensive and time consuming. Marker-assisted selection aims to find molecular markers that are linked to genes that determine quantitative traits of interest. Classical statistical methods require particular assumptions to be fulfilled, which is difficult to check if the analyses are performed automatically. In this article, we present a heuristic method to find interesting markers for quantitative traits. This method includes various strategies that depend on what makes a genotype interesting to a plant breeder. This approach was applied to eighteen parental lines of winter oilseed rape F₁ CMS ogura hybrids with observation of 597 markers. The traits of interest were seed yield and alkenyl glucosinolate content. Fifty-seven markers were selected for further study. The most prominent marker was OPY 02~1830. Marker-assisted selection is the first step of analysis, which can then be followed up by a more formal statistical analysis for a smaller set of interesting markers.     

Genotype-by-environment effects on the performance of recombinant inbred lines of Virginia-type peanut

Peanut (Arachis hypogaea L.) is known to be sensitive to genotype-by-environment interaction (GEI) effects. While previous studies have reported strong GEI effects on peanut yield, most of those studies involved a relatively small number of unrelated genotypes. We examined the extent of GEI effects in elite Virginia-type peanut using a large population of recombinant inbreed lines (RILs). Two-hundred-sixty-six F₇ RILs derived from different cultivars were grown in three environments. Net pod yield (NPY) was evaluated along with 11 other traits. ANOVA revealed that genotype and environment affected all of the examined traits, except for the triplet trait. The substantial influence of the environment was also demonstrated in a genetic-parameter analysis, in which the phenotypic variation coefficients were almost double those for genotypic variation. Still, relatively high heritability and genetic gain values were found for pod weight and NPY. Since NPY is the main target for selection, it was analyzed further. Path analysis showed that NPY is most directly influenced by pod weight and the shelling ratio. A significant GEI effect on NPY was identified using an AMMI model that described 42.7% of the total variation. This GEI component was subjected to a principal components analysis, which confirmed that the variability due to the different environments was greater than the variability that could be attributed to the different genotypes. Yet, several lines had stable yields across environments. These results demonstrate the importance of multi-location phenotyping for QTL analyses and crop improvement in peanut.     

Harvest index increase during seed growth of field pea

Harvest index during seed growth has been reported to increase linearly with time for many crop species. Although the rate of harvest index increase was generally stable across experiments within a species, there are indications that it is sensitive to variations in temperature. The objective of the present study was to compare the harvest index increase for field pea (Pisum sativum L.) across 31 experiments that included a wide range of temperature environments. The change in harvest index within each experiment was well described by a linear increase with time but there was considerable variability among experiments. The increase in harvest index was also calculated as a function of thermal time after flowering. The variability was only marginally reduced. Use of thermal time was, however, superior in identifying a common point for the initiation of seed growth among the experiments.     

Floral initiation in field-grown forage peas is delayed to a greater extent by short photoperiods, than in other types of European varieties

Frost is one of the main climatic stresses which has to be overcome by a winter pea crop. Some forage lines show a delayed floral initiation, which helps them to escape the main winter freezing periods, as a higher susceptibility to frost is observed after floral initiation commences. Frost tolerant forage peas have been used in all winter pea breeding programs in France and our main purpose was to evaluate to what extent those lines and the current winter varieties are variable for the date of floral initiation in field conditions. A field experiment was carried out during two years at the INRA experimental station of Mons (northern France). Different genotypes (9 in 1995–1996 and 12 in 1996–1997) were sown at approximately monthly intervals between September and June to provide a range of photothermal conditions. The date of floral initiation was determined by destructive sampling. We observed variability for the date of floral initiation among the different genotypes and sowing dates. Our data particularly highlighted the different reactions to photoperiod. Three varieties had no detectable reaction. Six varieties exhibited a quantitative response, with varied intensities. Lastly, the three forage varieties showed a qualitative, high response to photoperiod, which indicated the presence of the Hr allele, already described in Pisum. This revised version was published online in July 2006 with corrections to the Cover Date.     

田间试验的空间变异性及其统计控制

利用空间相关模型和传统方差分析模型对小麦和玉米3个田间试验产量数据进行了拟合与分析。结果表明，3个试验都显著存在空间变异，空间变异方差占据剩余变异方差的83.5%~0.4%；相对于传统随机完全区组分析法，空间相关模型法效应比较的标准误平均降低18.4%~14.2%，分析相对效率平均为1.50~1.36，因而比区组控制空间变异更有效；不同空间相关模型分析的结果呈现出一定的差异。建议利用空间相关模型分析田间试验，并利用Akaike信息准则（AIC）进行最佳空间相关模型选择。     

Transmission of a Bacillus thuringiensis cry3Aa transgene from diploid to tetraploid potato using 4x-2x hybridization: effect of ploidy increase on transgene expression and implications for TPS hybrid production

The study examined the effect of ploidy elevation through unreduced gametes on transgene expression in potato. Tetraploid transgenic progenies were obtained from one tetraploid potato cultivar crossed with 2n pollen producing diploid clones harbouring an exogenous transgene (cry3Aa). Both single‐ and multiple‐insert diploid transgenic lines that were regenerated by Agrobacterium tumefaciens leaf disc inoculation were used in crosses. A DAS‐ELISA system and no‐choice feeding bioassay enabled characterization of the parental lines as either ‘high’ or low’ expressers of the Cry3Aa protein. High Cry3Aa expression was observed for both single‐insert transgenic diploids and their 4x‐2x progeny. On the contrary, 68% of 4x‐2x progeny derived from a multiple‐insert, diploid transgenic had significantly reduced Cry3Aa expression compared with the parent, with 32% demonstrating nearly complete silencing of the transgene. Multiple copies of a transgene, like homologous native genes, may be susceptible to transgene silencing following polyploidization. Therefore, incorporation of exogenous transgenes into a true potato seed (TPS) production system is feasible if a single‐insert diploid parent is used. Gene‐centromere mapping of the cry3Aa transgene demonstrated that a non‐transgenic refuge might be naturally created in a TPS hybrid system through genetic recombination.     

Grain yield response and stability for oat lines with low-, medium-, and high-yielding ability

Summary Relationships that exist among grain yielding ability and response and stability of grain yields when tested over variable environments were examined. Two sets of oats lines were tested over many environments that had wide ranges in productivities. The lines in each set were divided into high-, medium-, and low-yielding groups on the basis of means across all environments, and variance components for genotype × environment interactions and means of regression responses and coefficients of determination were computed for the three yield categories in each set.Mean grain yields for the high-, medium-, and low-yielding groups across both sets of oats lines were 2.7, 2.3, and 1.9 Mg ha^-1, respectively. Coefficients of variability for the genotype × environment interaction were 18%, 16%, and 12% for the high-, medium-, and low-yielding categories, respectively. Means for regression responses were 1.22 for the high group, 0.99 for the medium, and 0.78 for the low. Most responses for the high and low groups were significantly different from 1.0. Means for coefficients of contingency were 0.63, 0.56, and 0.51 for the high-, medium-, and lowyielding groups, respectively.There was a positive relationship between mean grain yield and response of grain yield to improving environments. Thus, high yielding lines are also the responsive lines. Our study gave conflicting results about stability of production for the three yield groups. Coefficients of variation for genotype × environment interaction indicated that the high-yielding group was more interactive with environments than were the medium- and low-yielding ones: However, the means for coefficients of contingency indicated that the high yielding group was the most stable.Journal Paper No. J-12128 of the Iowa Agric. and Home Econ. Exp. Stn., Ames, IA 50011. Project 2447.     

普通小麦种内的一种细胞质变异

根据对小麦育种试验中25个正反杂交后代的调查,发现一些组合的正反杂交之间存在着一定差异,其中陕农17和矮丰三号正反杂交后代的育性分离显著不同。因此,用陕农17和矮丰三号及其同质近亲品系重复进行了正反杂交遗传试验。当以陕农17做母本与矮丰三号及其近亲品系杂交时,F₂代无雄性不育植株出现,然而,以矮丰三号等