Combining genotype, environment and attribute variables in regression models for predicting the cell-means of multi-environment cultivar trials

 The main objectives of this study were: (1) to develop models which combine variables of genotype, environment and attribute in regression models (GEAR) for increasing the accuracy of predicted cell-means of the genotype×environment two-way table, and (2) to compare GEAR models with the additive main effects and multiplicative interaction (AMMI) model. GEAR models were developed by regressing the observed values on principal components of genotypes (PCG) and environments (PCE). Genetic and environmental attributes were also added to the GEAR models. GEAR and AMMI models were applied to multi-environment trials of triticale (trial 1), maize (trial 2) and broad beans (trial 3). The random data-splitting and cross-validation procedure was used and the root mean square-predicted difference (RMSPD) was computed to validate each model. GEAR models increased the accuracy of predicted cell-means. Attribute variables, such as soil pH, rainfall, altitude and class of genotype, did not improve the best GEAR model of trial 1, but they increased the predictive value of other models. Two iterations of the computer program further refined the best GEAR model. Based on the RMSPD criterion, GEAR models were as good as, or better than, some AMMI truncated models for predicting cell-means. The approximate accuracy gain factors (GF) of the best GEAR model over the raw data were 2.08, 3.02 and 2.22, for trials 1, 2 and 3, respectively. The GF of the best AMMI model were 1.74, 2.28 and 2.32 for trials 1, 2 and 3, respectively. The analysis of variance of the predicted cell means showed that the genotype×environment interaction (GEI) variance was reduced by about 20% in trial 1 and 81% in trial 2. A bias associated with the predicted cell reduced the GEI variability. Advantages of using GEAR models in muti-environment cultivar trials are that they: (1) increase the precision of cell-mean estimates and (2) reduce the GEI variance and increase trait heritability. Received: 15 August 1997 / Accepted: 28 October 1997     

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. I. Timing of vegetative bud flush

Thirty three unique quantitative trait loci (QTLs) affecting the timing of spring bud flush have been identified in an intraspecific mapping population of coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii]. Both terminal and lateral bud flush were measured over a 4-year period on clonal replicates at two test sites, allowing for the repeated estimation of QTLs. QTLs were detected on 12 linkage groups and, in general, each explained a small proportion of the total phenotypic variance and were additive in effect. Several QTLs influence the timing of bud flush over multiple years, supporting earlier evidence that the timing of bud flush through developmental stages is under moderate to strong genetic control by the same suite of genes through developmental stages. However, only a few QTLs controlling the timing of bud flush were detected at both test sites, suggesting that geographic location plays a major role in the phenology of spring growth. A small number of QTLs with year and site interactions were also estimated. Received: 20 July 2000 / Accepted: 19 October 2000     

Nonlinear genotypic response to macro- and microenvironments

 Environmental variation can be due to macro- and microenvironments. Whereas macroenvironments, such as climate, density, and nutritional levels, are distinguishable, microenvironments including external random errors or internal “accidents” of an organism cannot be well specified. A quantitative genetic model is proposed to estimate the genetic control of response of genotypes to these two kinds of environments. The model extends Gimelfarb’s additive-multiplicative model for genotype×environment interaction by considering both macro- and microenvironmental variation and the mechanistic basis of genotypic response to a particular macroenvironmental factor. It is further extended to estimate genetic correlations between quantitative traits under the additive-multiplicative model. An example from a forest tree was used to illustrate the application and power of the new model. In many aspects, the model displays remarkable advantages over the traditional analysis of variance used to study genotype×environment interaction. Received: 15 July 1997 / Accepted: 19 September 1997     

Quantitative trait loci for grain quality, productivity, morphological and agronomical traits in sorghum (Sorghum bicolor L. Moench)

 Quantitative trait loci (QTLs) for grain quality, yield components and other traits were investigated in two Sorghum caudatum×guinea recombinant inbred line (RIL) populations. A total of 16 traits were evaluated (plant height, panicle length, panicle compactness, number of kernels/panicle, thousand-kernel weight, kernel weight/panicle, threshing percentage, dehulling yield, kernel flouriness, kernel friability, kernel hardness, amylose content, protein content, lipid content, germination rate and molds during germination and after harvest) and related to two 113- and 100-point base genetic maps using simple (SIM) and composite (CIM) interval mapping. The number, effects and relative position of QTLs detected in both populations were generally in agreement with the distributions, heritabilities and correlations among traits. Several chromosomal segments markedly affected multiple traits and were suspected of harbouring major genes. The positions of these QTLs are discussed in relation to previously reported studies on sorghum and other grasses. Many QTLs, depending on their relative effects and position, could be used as targets for marker-assisted selection and provide an opportunity for accelerating breeding programmes. Received: 14 February 1998 / Accepted: 4 March 1998     

Interpreting genotype × environment interaction in tropical maize using linked molecular markers and environmental covariables

An understanding of the genetic and environmental basis of genotype×environment interaction (GEI) is of fundamental importance in plant breeding. In mapping quantitative trait loci (QTLs), suitable genetic populations are grown in different environments causing QTLs×environment interaction (QEI). The main objective of the present study is to show how Partial Least Squares (PLS) regression and Factorial Regression (FR) models using genetic markers and environmental covariables can be used for studying QEI related to GEI. Biomass data were analyzed from a multi-environment trial consisting of 161 lines from a F_3:4 maize segregating population originally created with the purpose of mapping QTLs loci and investigating adaptation differences between highland and lowland tropical maize. PLS and FR methods detected 30 genetic markers (out of 86) that explained a sizeable proportion of the interaction of maize lines over four contrasting environments involving two low-altitude sites, one intermediate-altitude site, and one high-altitude site for biomass production. Based on a previous study, most of the 30 markers were associated with QTLs for biomass and exhibited significant QEI. It was found that marker loci in lines with positive GEI for the highland environments contained more highland alleles, whereas marker loci in lines with positive GEI for intermediate and lowland environments contained more lowland alleles. In addition, PLS and FR models identified maximum temperature as the most-important environmental covariable for GEI. Using a stepwise variable selection procedure, a FR model was constructed for GEI and QEI that exclusively included cross products between genetic markers and environmental covariables. Higher maximum temperature in low- and intermediate-altitude sites affected the expression of some QTLs, while minimum temperature affected the expression of other QTLs. Received: 10 January 1999 / Accepted: 12 March 1999     

Molecular mapping of the rf1 gene for pollen fertility restoration in sorghum (Sorghum bicolor L.)

We report the molecular mapping of a gene for pollen fertility in A1 (milo) type cytoplasm of sorghum using AFLP and SSR marker analysis. DNA from an F₂ population comprised of 84 individuals was screened with AFLP genetic markers to detect polymorphic DNAs linked to fertility restoration. Fifteen AFLP markers were linked to fertility restoration from the initial screening with 49 unique AFLP primer combinations (+3/+3 selective bases). As many of these AFLP markers had been previously mapped to a high-density genetic map of sorghum, the target gene (rf1) could be mapped to linkage group H. Confirmation of the map location of rf1 was obtained by demonstrating that additional linkage group-H markers (SSR, STS, AFLP) were linked to fertility restoration. The closest marker, AFLP Xtxa2582, mapped within 2.4 cM of the target loci while two SSRs, Xtxp18 and Xtxp250, flanked the rf1 locus at 12 cM and 10.8 cM, respectively. The availability of molecular markers will facilitate the selection of pollen fertility restoration in sorghum inbred-line development and provide the foundation for map-based gene isolation. Received: 22 August 2000 / Accepted: 18 October 2000     

Analysis of QTL×environment interaction for yield components and plant height in rice

 An F₂ and two equivalent F₃ populations of an indica-indica cross of rice, Tesanai 2/CB, were constructed and grown in different environments. The identification of quantitative trait loci (QTL) for yield components and plant height and an analysis of QTL×environment interaction were conducted for three trials. Interval mapping of QTL for eight traits was employed with a threshold of LOD=2 using the computer package MAPMAKER/QTL. A total of 44 QTL were detected in 18 intervals of nine chromosomes, including 3 for the number of panicles (NP), 5 for the number of filled grains (NFG), 6 for total number of spikelets (TNS), 3 for spikelet fertility (SF), 7 for 1000-grain weight (TGWT), 5 for grain weight per plant (GWT), 8 for plant height (PH) and 7 for panicle length (PL). The numbers of QTL detected in two or three trials were 1 for NP, 1 for NFG, 1 for TNS, none for SF, 4 for TGWT, 3 for GWT, 2 for PH and 5 for PL, making a total of 17. When a QTL was detected in more than one trial the direction and magnitude of its additive effect, the dominance effect and the degree of dominance were generally in good agreement. In all three trials, QTL were frequently detected for related traits in the same intervals. The directions of additive effect of QTL for related traits in a given interval were in agreement with few exceptions, no matter whether they were detected in the same trial or not. This result suggested that pleiotropism rather than close linkage of different QTL was the major reason why QTL for different traits were frequently detected in the same intervals. When gene pleiotropism was considered, 23 of the 29 QTL for yield and its components and 9 of the 15 QTL for plant stature were detected in more than one trial. This indicated that the detection of chromosomal segments harboring QTL was hardly affected by environmental factors. Received: 30 January 1997 / Accepted: 21 March 1997     

Towards a saturated sorghum map using RFLP and AFLP markers

 A near-saturated sorghum genetic linkage map was produced using RFLP, AFLP and morphological markers. First a composite, essentially RFLP-based genetic linkage map was obtained from analyses of two recombinant inbred populations. This map includes 343 loci for 11 linkage groups spanning 1352 cM. Since this map was constructed with many previously mapped heterologous probes, it offers a good basis for synteny studies. Separately, an AFLP map was obtained from the analysis of 168 bands revealed from 12 primer pair combinations. It includes 137 loci for 11 linkage groups spanning 849 cM. Taking into account the different data sets, we constructed a combined genetic linkage map including 443 loci spanning 1899 cM. Two main features are to be noted: (1) the distribution of AFLPs along the genome is not uniform; (2) an important stretching of the former core map is induced after adding the AFLPs. Received: 10 May 1998 / Accepted: 13 July 1998     

Marker-assisted selection with spatial analysis of unreplicated field trials

 Many studies have shown that molecular markers can improve the efficiency of the selection of quantitative traits in plant breeding provided that large population sizes are used. As a way to limit experimental costs it appears that the use of unreplicated trials may be more valuable than the use of replicated plots in one trial. In this particular context of unreplicated large trials, spatial heterogeneity within the field may reduce the efficiency of the selection. The problem of controlling spatial heterogeneity was seldom considered in the case of marker-assisted selection (MAS). Here, we propose an integrated method to predict genetic values considering simultaneously marker information and possible spatial heterogeneity. This method was applied to a population of 300 F₃ lines of maize evaluated in 11 unreplicated trials for grain yield. We show that when spatial field heterogeneity is considered through appropriate statistical models the accuracy of genetic value predictions is improved and the same genetic gain can be achieved with a reduced number of trials. Received: 7 January 1998 / Accepted: 20 July 1998     

A direct comparison between the genetic maps of sorghum and rice

A direct comparison of the genetic linkage maps of sorghum and rice is proposed. It is based on the mapping of a common set of 123 RFLP probes scattered on the genomes of both species. For each species a composite map was established by merging two individual maps comprising many common loci. This enabled us to confirm the global correspondence scheme that had previously been established between the chromosomes of sorghum and rice. It also provided a more detailed insight into the conservation of synteny and colinearity: 69% of the loci mapped on a given rice chromosome mapped to the corresponding homoeologous chromosome in sorghum; among them, 84% formed a colinear arrangement between the two species. Local inversions and translocations were detected. Received: 27 April 2000 / Accepted: 26 May 2000     

Adaptation of sorghum: characterisation of genotypic flowering responses to temperature and photoperiod

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop grown in a wide range of tropical and temperate environments. This study was conducted to characterise the photothermal flowering responses of sorghum genotypes and to examine relationships between photothermal characteristics and environment of origin in order to better understand the phenological basis of adaptation to environment in sorghum. Twenty-four germplasm accessions and one hybrid from 24 major sorghum-growing areas were grown in a wide range of environments varying in temperature and photoperiod in India, Kenya and Mali between 1992 and 1995. Times from sowing to flowering (f) were recorded, and the responsiveness of 1/f to temperature and photoperiod was quantified using photothermal models. Times from sowing to flowering were accurately predicted in a wide range of environments using a multiplicative rate photothermal model. Significant variation in the minimum time to flower (F_m) and photoperiod sensitivity (critical photoperiod, P_c, and photoperiod-sensitivity slope, P_s) was observed among the genotypes; in contrast there was little variation in base temperature (T_b). Adaptation of sorghum to the diverse environments in which it is grown was largely determined by photoperiod sensitivity and minimum time to flower; photoperiod sensitivity determines broad adaptation to latitude (daylength), while variation in the minimum time to flower determines specific adaptation within smaller ranges of latitude, e.g. within the humid and sub-humid tropics. Received: 16 January 1999 / Accepted: 11 March 1999     

Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid

 A sorghum composite linkage map was constructed with two recombinant inbred line populations using heterologous probes already mapped on maize and sugarcane. This map includes 199 loci revealed by 188 probes and distributed on 13 linkage groups. A comparison based on 84 common probes was performed between the sorghum composite map and a map of a sugarcane (Saccharum spp.) cultivar being developed and presently comprising 10 tentative linkage groups. A straight synteny was observed for 2 pairs of linkage groups; in two cases, 1 sorghum linkage group corresponded to 2 or 3 sugarcane linkage groups, respectively; in two cases 1 sugarcane link- age group corresponded to 2 separate sorghum linkage groups; for 2 sorghum linkage groups, no complete correspondance was found in the sugarcane genome. In most cases loci appeared to be colinear between homoeologous chromosomal segments in sorghum and sugarcane. These results are discussed in relation to published data on sorghum genomic maps, with specific reference to the genetic organization of sugarcane cultivars, and they, illustrate how investigations on relatively simple diploid genomes as sorghum will facilitate the mapping of related polyploid species such as sugarcane. Received: 12 August 1996 / Accepted: 30 August 1996     

Mitochondrial and total DNA RAPD patterns can distinguish restorers of CMS lines in sorghum

 Seven sorghum restorer lines that differentially restore (or maintain) the A1 and A2 cytoplasmic male-sterile (CMS) cytoplasms were studied by RFLP analyses of their mtDNAs and RAPD analyses of their mitochondrial DNA (mtDNA) and total DNA to understand nuclear mitochondrial combinations that are present in these lines. RFLP data from 11 mitochondrial gene probes were inadequate to classify these seven lines. However, the analysis of RAPD profiles of total DNA could distinguish these lines on the basis of their ability to restore completely or partially the fertility in the A1/A2 CMS cytoplasms. Interestingly, RAPD profiles of mtDNAs of these lines also followed the same pattern as that of the total DNA. These results indicate that the different restorer lines possess specific nuclear-cytoplasm combinations. Further, the results also show that the RAPD technique can be used to identify markers for different cytoplasms used in CMS. Received: 26 August 1997 / Accepted: 9 October 1997     

Identification of genomic regions that affect grain-mould incidence and other traits of agronomic importance in sorghum

Grain-mould is a major problem in grain sorghum utilization as mouldy grain has a reduced quality due to the deterioration of the endosperm and reduced embryo viability. Here, our objective was to use genome mapping to improve knowledge of genetic variation and co-variation for grain-mould incidence and other inter-related agronomic traits. Grain-mould incidence, kernel-milling hardness, grain density, plant height, panicle peduncle length, foliar-disease incidence, and plant color were measured on 125 F₅ genotypes derived from a cross of Sureño and RTx430. Quantitative trait loci were detected by means of 130 mapped markers (44 microsatellites, 85 AFLPs, one morphological-trait locus) distributed among ten linkage groups covering 970 cM. One to five QTLs affected each trait, with the exception of grain density for which no QTLs were detected. Grain-mould incidence was affected by five QTLs each accounting for between 10 and 23% of the phenotypic variance. The effects and relative positions of QTLs for grain-mould incidence were in accordance with the QTL distribution of several inter-related agronomic traits (e.g., plant height, peduncle length) and with the correlation between these phenotypic traits and grain-mould incidence. The detection of QTLs for grain-mould incidence was dependent on the environment, which is consistent with heritibility estimates that show strong environmental and genotype × environment effects. Several genomic regions affected multiple traits including one region that affected grain-mould incidence, plant height, panicle peduncle length, and grain-milling hardness, and a second region that influenced grain-mould (in four environments) and plant height. One genomic region, which harbors loci for plant color, influenced the severity of foliar disease symptoms and the incidence of grain-mould in one environment. Collectively QTLs detected in the present population explained between 10% and 55% of the phenotypic variance observed for a given trait.     

Studies of iron transport by arbuscular mycorrhizal hyphae from soil to peanut and sorghum plants

 The influence of an arbuscular mycorrhizal (AM) fungus on phosphorus (P) and iron (Fe) uptake of peanut (Arachis hypogea L.) and sorghum (Sorghum bicolor L.) plants was studied in a pot experiment under controlled environmental conditions. The plants were grown for 10 weeks in pots containing sterilised calcareous soil with two levels of Fe supply. The soil was inoculated with rhizosphere microorganisms only or with rhizosphere microorganisms together with an AM fungus (Glomus mosseae [Nicol. & Gerd.] Gerdemann & Trappe). An additional small soil compartment accessible to hyphae but not roots was added to each pot after 6 weeks of plant growth. Radiolabelled P and Fe were supplied to the hyphae compartment 2 weeks after addition of this compartment. After a further 2 weeks, plants were harvested and shoots were analysed for radiolabelled elements. In both plant species, P uptake from the labelled soil increased significantly more in shoots of mycorrhizal plants than non-mycorrhizal plants, thus confirming the well-known activity of the fungus in P uptake. Mycorrhizal inoculation had no significant influence on the concentration of labelled Fe in shoots of peanut plants. In contrast, ⁵⁹Fe increased in shoots of mycorrhizal sorghum plants. The uptake of Fe from labelled soil by sorghum was particularly high under conditions producing a low Fe nutritional status of the plants. These results are preliminary evidence that hyphae of an arbuscular mycorrhizal fungus can mobilise and/or take up Fe from soil and translocate it to the plant. Accepted: 6 March 1998     

Comparative mapping of QTLs for agronomic traits of rice across environments by using a doubled-haploid population

We report here the RFLP mapping of quantitative trait loci (QTLs) which affect some important agronomic traits in cultivated rice. An anther culture-derived doubled-haploid (DH) population was established from a cross between indica and japonica rice varieties. A molecular linkage map comprising 137 markers was constructed based on this population which covered the rice genome at intervals of 14.8 cM on average. The linkage map was used to locate QTLs for such important agronomic traits as heading date, plant height, number of spikelets per panicle, number of grains per panicle, 1 000-grain weight and the percentage of seed set, by interval mapping. Evidence of genotype-by-environment interaction was found by comparing QTL maps of the same population grown in three diverse environments. A total of 22 QTLs for six agronomic traits was detected which were significant in at least one environment, but only seven were significant in all three environments; seven were significant in two environments and eight could only be detected in a single environment. However, QTLs-by-environment interaction was trait dependent. QTLs for spikelets and grains per panicle were common across environments while traits like heading date and plant height were more sensitive to environment. Received: 22 February 1996 / Accepted: 10 May 1996     

QTLs for agronomic traits from a Mediterranean barley progeny grown in several environments

In order to identify quantitative trait loci (QTLs) controlling agronomic trait variation and their consistency under Mediterranean conditions in barley, a progeny of 167 recombinant inbred lines (RILs) and the parents Tadmor and Er/Apm, originating from the Mediterranean basin, were grown under Mediterranean conditions in 1995, 1996, 1997 and 1999. For the 2 first years (M95 and G96), one replicate was grown, but for the latter (M97 and M99) two rainfed (rain) and two irrigated (ir) replicates were produced. M95, G96, M97rain, M97ir, M99rain and M99ir were considered as six different environments and were compared in terms of their meteorological conditions and water supply. Grain yield and yield components were assessed, as well as heading date and plant height. Highly significant differences were noted between environments. QTLs were obtained from each environment separately and from a multiple environment analysis (simple interval mapping and simplified composite interval mapping). Despite heterogeneity between environments, numerous QTLs were common to several environments. This was particularly true for traits like plant height and thousand-grain weight. The most reliable QTLs which explained the largest part of the phenotypic variation were obtained for plant height on chromosomes 3 (3H) and 6 (6H). The multiple-environment analysis provided an opportunity to identify consistent QTLs for agronomic traits over six Mediterranean environments. A total of 24 consistent QTLs were detected. Out of these, 11 presented main effects, seven presented QTL×E interaction, and six presented both effects. In addition, 18 of the consistent QTLs were common to other published work and six seemed specific to this study. These latter QTLs could be involved in Mediterranean adaptive specificities or could be specific to the studied genetic background. Finally, when the rainfed and the irrigated environments of M97 were considered separately, a total of 16 QTLs presenting main effects over the two water conditions were identified, whereas five QTLs seemed dependent on the water conditions. Received: 31 January 2001 / Accepted: 19 February 2001     

Culture and regeneration of mesophyll-derived protoplasts of sorghum [Sorghum bicolor (L.) Moench]

 A protocol for plant regeneration from mesophyll/protoplasts of sorghum [Sorghum bicolor (L.) Moench] was developed. The yield of intact protoplasts, their subsequent divisions and regeneration were genotype-dependent. The genotype 296B was always more responsive than IS 32266. For 296B, the sixth leaf from 18-day-old plants kept in dark for 2 days before harvesting was found to be the most suitable source of viable protoplasts. The first division was observed 10–12 days after plating, and the second division after 12–14 days. The maximum plating efficiency was 4.8% in 296 B, followed by 2.48% in IS 32266. Microcolonies were visible after 25–30 days, and microcalli after 60–75 days. Whole plants were obtained after 6–8 weeks of culture of microcalli on MS medium containing 0.2 mg l^–1 kinetin and 2 mg l^–1 BAP. The frequency of regeneration in 296B and IS 32266 was 12.80% and 10.58%, respectively. Ten plants transferred to pots in the glasshouse established well. The seeds collected from glasshouse-grown plants were sown in the field where plants were grown to maturity. Received: 7 October 1998 / Revision received: 13 January 1999 / Accepted: 20 January 1999