Quantitative trait loci for the stay green trait in sorghum (Sorghum bicolor L. Moench): consistency across genetic backgrounds and environments

 Stay green in sorghum (Sorghum bicolor L. Moench) is characterized by the plant’s ability to tolerate post-flowering drought stress, thereby delaying the premature leaf and plant death. It contributes to normal grain filling and reduces the incidence of stalk lodging and charcoal rot disease during the late stages of grain development. Breeding for improving post-flowering drought tolerance in sorghum hybrids remains an important objective of sorghum breeders. Since evaluation of the stay green response is difficult and unreliable under field conditions, due to the timing and intensity of moisture stress and large environmental interaction, progress in improving drought tolerance by conventional breeding methods has been slow. The objective of the present study was to determine the consistency of quantitative trait loci (QTLs) controlling stay green in sorghum. We re-evaluated the Recombinant Inbred Line (RIL)-mapping population from the cross B35 x Tx7000 in two locations over 2 years and compared it with earlier reports. Analysis using the combined stay green-rating means of seven environments and the expanded molecular map reconfirmed all four stay green QTLs (Stg1, Stg2, Stg3 and Stg4) that were identified earlier by Xu et al. (2000). Similarly, comparison of the stay green QTL locations with earlier reported results indicated that all four stay green QTLs showed consistency across different genetic backgrounds. Examination of the stay green QTL profiles of the best and poorest stay-green lines indicated that three stay green QTLs, Stg1, Stg2 and Stg3, appear to be important for the expression of this trait when the percent phenotypic variation, and the consistency in different backgrounds and different environments, are considered. A significant epistatic interaction involving Stg2 and a region on linkage group C was also identified for the stay green and chlorophyll content. We concluded that Stg2 is the most important QTL controlling stay green, explaining the maximum amount of phenotypic variation. This report further strengthens our view to target the Stg2 QTL region for gene discovery in order to improve the basic understanding of the stay green phenomenon, which might be helpful in manipulating this trait not only in sorghum but also in other cereal crop species. Received: 12 January 2000 / Accepted: 12 February 2000     

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.     

Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench)

Drought is a major constraint in sorghum production worldwide. Drought-stress in sorghum has been characterized at both pre-flowering and post-flowering stages resulting in a drastic reduction in grain yield. In the case of post-flowering drought stress, lodging further aggravates the problem resulting in total loss of crop yield in mechanized agriculture. The present study was conducted to identify quantitative trait loci (QTLs) controlling post-flowering drought tolerance (stay green), pre-flowering drought tolerance and lodging tolerance in sorghum using an F₇ recombinant inbred line (RIL) population derived from the cross SC56×Tx7000. The RIL lines, along with parents, were evaluated for the above traits in multiple environments. With the help of a restriction fragment length polymorphism (RFLP) map, which spans 1,355 cM and consists of 144 loci, nine QTLs, located over seven linkage groups were detected for stay green in several environments using the method of composite interval mapping. Comparison of the QTL locations with the published results indicated that three QTLs located on linkage groups A, G and J were consistent. This is considered significant since the stay green line SC56 used in our investigation is from a different source compared to B35 that was used in all the earlier investigations. Comparative mapping has shown that two stay green QTLs identified in this study corresponded to stay green QTL regions in maize. These genomic regions were also reported to be congruent with other drought-related agronomic and physiological traits in maize and rice, suggesting that these syntenic regions might be hosting a cluster of genes with pleiotropic effects implicated in several drought tolerance mechanisms in these grass species. In addition, three and four major QTLs responsible for lodging tolerance and pre-flowering drought tolerance, respectively, were detected. This investigation clearly revealed the important and consistent stay green QTLs in a different stay green source that can logically be targeted for positional cloning. The identification of QTLs and markers for pre-flowering drought tolerance and lodging tolerance will help plant breeders in manipulating and pyramiding those traits along with stay green to improve drought tolerance in sorghum. Received: 2 June 2000 / Accepted: 15 November 2000     

Isolation,characterization, and mapping of the stay green mutant in rice

Leaf color turns yellow during senescence due to the degradation of chlorophylls and photosynthetic proteins. A stay green mutant was isolated from the glutinous japonica rice Hwacheong-wx through N-methyl-N-nitrosourea mutagenesis. Leaves of the mutant remained green, while turning yellow in those of the wild-type rice during senescence. The stay green phenotype was controlled by a single recessive nuclear gene, tentatively symbolized as sgr(t). All the phenotypic characteristics of the mutant were the same as those of the wild-type lines except for the stay green trait. The leaf chlorophyll concentration of the mutant was similar to that of the wild-type before heading, but decreased steeply in the wild-type during grain filling, while very slowly in the mutant. However, no difference in photosynthetic activity was observed between the stay green mutant and the yellowing wild-type leaves, indicating that senescence is proceeding normally in the mutant leaves and that the mutation affects the rate of chlorophyll degradation during the leaf senescence. Using phenotypic and molecular markers, we mapped the sgr(t) locus to the long arm of chromosome 9 between RFLP markers RG662 and C985 at 1.8- and 2.1-cM intervals, respectively. Received: 29 April 2001 / Accepted: 17 July 2001     

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     

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     

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     

Simultaneous marker-assisted selection for multiple traits in autogamous crops

A method is presented for the selection of parents with the aim of obtaining improved genotypes in the progeny of a cross. The procedure is designed to select in several unrelated traits simultaneously and is based on the selection of molecular markers that are linked to QTLs. The method was compared with conventional phenotypic selection in simulation experiments for a number of genetic structures underlying the traits and several types of parental populations. Although the method in general provides good results, some of the underlying assumptions may be violated quite easily, thereby reducing the applicability of the procedure in practice. Received: 10 September 1999 / Accepted: 24 August 2000     

Identification of genomic regions affecting plant height in sorghum and maize

The objective of this study was to use restriction fragment length polymorphisms (RFLPs) to determine the genetic location and effects of genomic regions controlling plant height in sorghum. F₂ plants (152) from the cross CK60 x PI229828 were used. Genomic and cDNA clones (106) identified 111 loci distributed among ten linkage groups covering 1299 cM. Interval mapping identified four regions, each in a separate linkage group. These regions may correspond to loci (dw) previously identified by alleles with qualitative effects. Also, these regions identified in sorghum may be orthologous to those previously reported for plant height in maize. Gene effects and gene action varied among genomic regions. In each region, PI229828 alleles resulted in increased plant height. Each region accounted for 9.2–28.7% of the phenotypic variation. Positive, additive effects ranged from 15 to 32cm. Tallness was dominant or overdominant and conferred by alleles from PI229828 for three quantitative trait loci (QTL). At the fourth QTL, PI229828 contributed to increased plant height, but short stature was partially dominant. One digenic interaction was significant. The presence of a PI229828 allele at one region diminished the effects of the other region. A multiple model indicated that these four regions collectively accounted for 63.4% of the total phenotypic variation. The utility of this information for germplasm conversion through backcross breeding is discussed.Journal Paper No. J. 15649 of the Iowa Agriculture and Home Economic Experiment Station, Ames, Iowa. Project No. 3134     

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     

Identification of RAPD markers for 11 Hessian fly resistance genes in wheat

 The pyramiding of genes that confer race- or biotype-specific resistance has become increasingly attractive as a breeding strategy now that DNA-based marker-assisted selection is feasible. Our objective here was to identify DNA markers closely linked to genes in wheat (Triticum aestivum L.) that condition resistance to Hessian fly [Mayetiola destructor (Say)]. We used a set of near-isogenic wheat lines, each carrying a resistance gene at 1 of 11 loci (H3, H5, H6, H9, H10, H11, H12, H13, H14, H16 or H17) and developed by backcrossing to the Hessian fly-susceptible wheat cultivar ‘Newton’. Using genomic DNA of these 11 lines and ‘Newton’, we have identified 18 randomly amplified polymorphic DNA (RAPD) markers linked to the 11 resistance genes. Seven of these markers were identified by denaturing gradient gel electrophoresis and the others by agarose gel electrophoresis. We confirmed linkage to the Hessian fly resistance loci by cosegregation analysis in F₂ populations of 50–120 plants for each different gene. Several of the DNA markers were used to determine the presence/absence of specific Hessian fly resistance genes in resistant wheat lines that have 1 or possibly multiple genes for resistance. The use of RAPD markers presents a valuable strategy for selection of single and combined Hessian fly resistance genes in wheat improvement. Received: 20 March 1996 / Accepted: 6 September 1996     

Quantitative trait dissection analysis in Eucalyptus using RAPD markers: 1. Detection of QTL in interspecific hybrid progeny, stability of QTL expression across different ages

 The objective of this study was to use random amplified polymorphic DNA (RAPD) to determine the genetic location and effects of genomic regions controlling wood density, stem growth and stem form in two species of Eucalyptus. Two hundred F₁ trees generated from an interspecific cross E. urophylla×E. grandis between two elite trees were used. Genetic maps were constructed for each parent with markers segregating in the 1:1 ratio in FS progeny. A total of 86 and 92 markers distributed among 11 linkage groups covered 1295 cM and 1312 cM for the E. urophylla and E. grandis parent, respectively. Traits were measured three times up to selection age (38 months). The magnitude of the phenotypic variation explained by the joint action of the segregating quantitative trait alleles indicated that genetic factors of large effect were involved in the control of the studied characters. Several regions controlling part of the variation for the studied traits were identified by interval mapping. Some regions of the genome exerted effects on more than one trait, providing a genetic explanation for at least some of the correlation between the traits. On the basis of an age-by-age analysis, a partial stability of QTL expression was observed with 68% of the QTL being expressed at two ages and 32% being age-specific. No QTL were significant for all three ages. Taking advantage of repeated measurements on the same material across different ages, we investigated with a maximum statistical power, the effect of marker genotype on traits, with age and QTL×age interaction effects being removed. A two-way analysis of variance made it possible to detect significant marker-trait associations over the period studied. Most of them had already been detected in the annual analysis. This result is very encouraging for the application of marker information to the early selection of hybrid trees to be vegetatively propagated for the production of clonal varieties. Received: 2 December 1996/Accepted: 4 April 1997     

Mapping and validation of chromosome regions conferring boron toxicity tolerance in wheat (Triticum aestivum)

Boron is an essential plant micro-nutrient which can be phytotoxic to plants if present in soils in high concentration. Boron toxicity has been recognised as an important problem limiting production in the low rainfall areas of southern Australia, West Asia and North Africa. Genetic variation for boron toxicity tolerance in wheat has been well-characterised. The efficiency of breeding for boron toxicity tolerance could be greatly enhanced by the development of molecular markers associated with QTLs for tolerance in wheat. A population of 161 doubled haploids from a cross between the tolerant cultivar Halberd and the moderately sensitive cultivar Cranbrook was used to identify chromosomal regions involved in boron tolerance. A combined RFLP and AFLP linkage map of the Cranbrook x Halberd population was used to identify chromosomal regions involved in the boron tolerance traits measured. Regions on chromosome 7B and 7D were associated with leaf symptom expression. The region on chromosome 7B was also associated with the control of boron uptake and with a reduction in the effect of boron toxicity on root-growth suppression. RFLP markers at the chromosome 7B and 7D loci were shown to be effective in selecting for improved boron tolerance in an alternative genetic background. Halberd alleles at the chromosome 7B locus were associated with the concentration of boron in whole shoots and grain. The concentration of boron in whole shoots and in grain were both related to grain yield in a field trial conducted on soil containing toxic levels of boron. Implications relating to marker-assisted selection for boron toxicity tolerance in wheat are discussed. Received: 3 September 1999 / Accepted: 12 February 2000     

Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought-stress conditions

Drought stress during the reproductive stage is one of the most important environmental factors reducing the grain yield and yield stability of pearl millet. A QTL mapping approach has been used in this study to understand the genetic and physiological basis of drought tolerance in pearl millet and to provide a more-targeted approach to improving the drought tolerance and yield of this crop in water-limited environments. The aim was to identify specific genomic regions associated with the enhanced tolerance of pearl millet to drought stress during the flowering and grain-filling stages. Testcrosses of a set of mapping-population progenies, derived from a cross of two inbred pollinators that differed in their response to drought, were evaluated in a range of managed terminal drought-stress environments. A number of genomic regions were associated with drought tolerance in terms of both grain yield and its components. For example, a QTL associated with grain yield per se and for the drought tolerance of grain yield mapped on linkage group 2 and explained up to 23% of the phenotypic variation. Some of these QTLs were common across stress environments whereas others were specific to only a particular stress environment. All the QTLs that contributed to increased drought tolerance did so either through better than average maintenance (compared to non-stress environments) of harvest index, or harvest index and biomass productivity. It is concluded that there is considerable potential for marker-assisted backcross transfer of selected QTLs to the elite parent of the mapping population and for their general use in the improvement of pearl millet productivity in water-limited environments. Received: 15 November 2000 / Accepted: 12 April 2001     

A model for marker-assisted selection among single crosses with multiple genetic markers

 Trait means of marker genotypes are often inconsistent across experiments, thereby hindering the use of regression techniques in marker-assisted selection. Best linear unbiased prediction based on trait and marker data (TM-BLUP) does not require prior information on the mean effects associated with specific marker genotypes and, consequently, may be useful in applied breeding programs. The objective of this paper is to present a flanking-marker, TM-BLUP model that is applicable to interpopulation single crosses that characterize maize (Zea mays L.) breeding programs. The performance of a single cross is modeled as the sum of testcross additive and dominance effects at unmarked quantitative trait loci (QTL) and at marked QTL (MQTL). The TM-BLUP model requires information on the recombination frequencies between flanking markers and the MQTL and on MQTL variances. A tabular method is presented for calculating the conditional probability that MQTL alleles in two inbreds are identical by descent given the observed marker genotypes (G ^k _obs) at the kth MQTL. Information on identity by descent of MQTL alleles can then be used to calculate the conditional covariance of MQTL effects between single crosses given G ^k _obs. The inverse of the covariance matrix for dominance effects at unmarked QTL and MQTL can be written directly from the inverse of the covariance matrices of the corresponding testcross additive effects. In practice, the computations required in TM-BLUP may be prohibitive. The computational requirements may be reduced with simplified TM-BLUP models wherein dominance effects at MQTL are excluded, only the single crosses that have been tested are included, or information is pooled across several MQTL. Received: 22 June 1997 / Accepted: 25 February 1998     

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     

Identification of RAPD markers linked to a locus involved in quantitative resistance to TYLCV in tomato by bulked segregant analysis

 In tomato, Bulked Segregant Analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to a quantitative trait locus (QTL) involved in the resistance to the Tomato Yellow Leaf Curl Virus. F₄ lines were distributed into two pools, each consisting of the most resistant and of the most susceptible individuals, respectively. Both pools were screened using 600 random primers. Four RAPD markers were found to be linked to a QTL responsible for up to 27.7% of the resistance. These markers, localized in the same linkage group within a distance of 17.3 cM, were mapped to chromosome 6 on the tomato RFLP map. Received: 21 August 1996 / Accepted: 4 April 1997     

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     

Two simple sequence repeat markers to select for soybean cyst nematode resistance coditioned by the rhg1 locus

The soybean cyst nematode (SCN) (Heterodera glycines Inchinoe) is the most economically significant soybean pest. The principal strategy to reduce or eliminate damage from this pest is the use of resistant cultivars. Identifying resistant segregants in a breeding program is a difficult and expensive process which is complicated by the oligogenic nature of the resistance and genetic variability in the pathogen. Fortunately, resistance at one SCN-resistance locus, rhg1, is generally accepted as a necessity for the development of resistant genotypes using any source of resistance and when challenged by any SCN race. Thus, the development of SCN resistant cultivars would be expedited if an effective and rapid system were available to identify breeding lines carrying a resistance allele at the rhg1 locus. In this study we report two simple sequence repeat (SSR) or microsatellite loci that cosegregate and map 0.4 cM from rhg1. Allelic variation at the first of these loci, BARC-Satt309, distinguished most, if not all, SCN-susceptible genotypes from those carrying resistance at rhg1 derived from the important SCN-resistance sources ’Peking’, PI 437654, and PI 90763. BARC-Satt309 was also effective in distinguishing SCN resistance sources PI 88788 and PI 209332 from many, but not all, susceptible genotypes. BARC-Satt309 cannot be used in marker-assisted selection in populations developed from typical southern US cultivars crossed with the important resistance sources PI 88788 or PI 209332 because these genotypes all carry the identical allele at the BARC-Satt309 locus. A second SSR locus, BARC-Sat_168, was developed from a bacterial artificial chromosome (BAC) clone that was identified using the primers to BARC-Satt309. BARC-Sat_168 distinguished PI 88788 and PI 209332 from southern US cultivars such as ’Lee’, ’Bragg’ and ’Essex’. Both BARC-Satt309 and BARC-Sat_168 were used to assay lines from SCN-susceptible×SCN-resistant crosses and proved to be highly effective in identifying lines carrying rhg1 resistance from those carrying the allele for SCN susceptibility at the rhg1 locus. Received: 5 November 1998 / Accepted: 3 February 1999