Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program

Seventy sorghum inbred lines which formed part of the Queensland Department of Primary Industries (QDPI) sorghum breeding program were screened with 104 previously mapped RFLP markers. The lines were related by pedigree and consisted of ancestral source lines, intermediate lines and recent releases from the program. We compared the effect of defining marker alleles using either identity by state (IBS) or identity by descent (IBD) on our capacity to trace markers through the pedigree and detect evidence of selection for particular alleles. Allelic identities defined using IBD were much more sensitive for detecting non-Mendelian segregation in this pedigree. Only one marker allele showed significant evidence of selection when IBS was used compared with ten regions with particular allelic identities when IBD was used. Regions under selection were compared with the location of QTLs for agronomic traits known to be under selection in the breeding program. Only two of the ten regions were associated with known QTLs that matched with knowledge of the agronomic characteristics of the ancestral lines. Some of the other regions were hypothesised to be associated with genes for particular traits based on the properties of the ancestral source lines.     

Inheritance of osmotic adjustment to water stress in three grain sorghum crosses

Water stress is one of the major constraints to the grain yield of sorghum in tropical and sub-tropical areas of the world. Osmotic adjustment has been widely proposed as a plant attribute that confers adaptation to water stress. The inheritance of osmotic adjustment to water stress was investigated in a series of generations derived from the three possible bi-parental crosses between two inbred sorghum lines with a high capacity for osmotic adjustment (Tx2813 and TAM422; high-OA lines) and one with a low capacity (QL27; low-OA line). Broad-sense heritability on a single-plant basis was generally found to be high. Analysis of segregation ratios by the mixture method of clustering identified two independent major genes for high osmotic adjustment. The line Tx2813 possessed a recessive gene which is given the symbol oa1; the line TAM422 possessed an additive gene which is given the symbol OA2. There was some evidence that there may be other minor genes which influence the expression of osmotic adjustment in these crosses as two putative transgressive segregants, with higher osmotic adjustment than the parents, were identified from the cross between Tx2813 and TAM422. Populations of recombinant inbred lines were developed and characterised for osmotic adjustment for two of the crosses (QL27 x TAM422, low-OA x high-OA; Tx2813 x TAM422, high-oal x high-OA2). These will be used to conduct experiments which test hypotheses about the contribution of the high-osmotic-adjustment genes to the grain yield of sorghum under a range of water-stress conditions.     

Mapping and characterization of Rf 5: a new gene conditioning pollen fertility restoration in A1 and A2 cytoplasm in sorghum (Sorghum bicolor (L.) Moench)

With an aim to further characterize the cytoplasmic male sterility–fertility restoration system in sorghum, a major fertility restoration gene was mapped along with a second locus capable of partial restoration of pollen fertility. The major fertility restoration gene, Rf ₅ , was located on sorghum chromosome SBI-05, and was capable of restoring pollen fertility in both A₁ and A₂ male sterile cytoplasms. Depending on the restorer parent, mapping populations exhibited fertility restoration phenotypes that ranged from nearly bimodal distribution due to the action of Rf ₅ , to a more normalized distribution reflecting the action of Rf ₅ and additional modifier/partial restoration genes. A second fertility restoration locus capable of partially restoring pollen fertility in A₁ cytoplasm was localized to chromosome SBI-04. Unlike Rf ₅ , this modifier/partial restorer gene acting alone resulted in less than 10% seed set in both A₁ and A₂ cytoplasms, and modified the extent of restoration conditioned by the major restorer Rf ₅ in A₁ cytoplasm. In examining the genomic regions spanning the Rf ₅ locus, a cluster of pentatricopeptide gene family members with high homology to rice Rf ₁ and sorghum Rf ₂ were identified as potential candidates encoding Rf ₅ .     

Molecular characterization of the waxy locus in sorghum

A comparison of approximately 4.5 kb of nucleotide sequence from the waxy locus (the granule-bound starch synthase I [GBSS I] locus) from a waxy line, BTxARG1, and a non-waxy line, QL39, revealed an extremely high level of sequence conservation. Among a total of 24 nucleotide differences and 9 indels, only 2 nucleotide changes resulted in altered amino acid residues. Protein folding prediction software suggested that one of the amino acid changes (Glu to His) may result in an altered protein structure, which may explain the apparently inactive GBSS I present in BTxARG1. This SNP was not found in the second waxy line, RTx2907, which does not produce GBSS I, and no other SNPs or indels were found in the approximately 4 kb of sequence obtained from RTx2907. Using one indel, the waxy locus was mapped to sorghum chromosome SBI-10, which is syntenous to maize chromosome 9; the waxy locus has been mapped to this maize chromosome. The distribution of indels in a diverse set of sorghum germplasm suggested that there are two broad types of non-waxy GBSS I alleles, each type comprising several alleles, and that the two waxy alleles in BTxARG1 and RTx2907 have evolved from one of the non-waxy allele types. The Glu/His polymorphism was found only in BTxARG1 and derived lines and has potential as a perfect marker for the BTxARG1 source of the waxy allele at the GBSS I locus. The indels correctly predicted the non-waxy phenotype in approximately 65% of diverse sorghum germplasm. The indels co-segregated perfectly with phenotype in two sorghum populations derived from crosses between a waxy and a non-waxy sorghum line, correctly identifying heterozygous lines. Thus, these indel markers or sequence-based SNP markers can be used to follow waxy alleles in sorghum breeding programs in selected pedigrees.     

Molecular mapping and candidate gene identification of the Rf2 gene for pollen fertility restoration in sorghum [Sorghum bicolor (L.) Moench]

The A1 cytoplasmic–nuclear male sterility system in sorghum is used almost exclusively for the production of commercial hybrid seed and thus, the dominant genes that restore male fertility in F₁ hybrids are of critical importance to commercial seed production. The genetics of fertility restoration in sorghum can appear complex, being controlled by at least two major genes with additional modifiers and additional gene–environment interaction. To elucidate the molecular processes controlling fertility restoration and to develop a marker screening system for this important trait, two sorghum recombinant inbred line populations were created by crossing a restorer and a non-restoring inbred line, with fertility phenotypes evaluated in hybrid combination with three unique cytoplasmic male sterile lines. In both populations, a single major gene segregated for restoration which was localized to chromosome SBI-02 at approximately 0.5 cM from microsatellite marker, Xtxp304. In the two populations we observed that approximately 85 and 87% of the phenotypic variation in seed set was associated with the major Rf gene on SBI-02. Some evidence for modifier genes was also observed since a continuum of partial restored fertility was exhibited by lines in both RIL populations. With the prior report (Klein et al. in Theor Appl Genet 111:994–1012, 2005) of the cloning of the major fertility restoration gene Rf1 in sorghum, the major fertility restorer locus identified in this study was designated Rf2. A fine-mapping population was used to resolve the Rf2 locus to a 236,219-bp region of chromosome SBI-02, which spanned ~31 predicted open reading frames including a pentatricopeptide repeat (PPR) gene family member. The PPR gene displayed high homology with rice Rf1. Progress towards the development of a marker-assisted screen for fertility restoration is discussed.     

Prediction of hybrid performance in grain sorghum using RFLP markers

Heterosis is an important component of hybrid yield performance. Identifying high yielding hybrids is expensive and involves testing large numbers of hybrid combinations in multi-environment trials. Molecular marker diversity has been proposed as a more efficient method of selecting superior combinations. The aim of this study was to investigate the value of molecular marker-based distance information to identify high yielding grain sorghum hybrids in Australia. Data from 48 trials were used to produce hybrid performance-estimates for four traits (yield, height, maturity and stay green) for 162 hybrid combinations derived from 70 inbred parent lines. Each line was screened with 113 mapped RFLP markers. The Rogers distances between the parents of each hybrid were calculated from the marker information on a genome basis and individually for each of the ten linkage groups of sorghum. Some of the inbred parents were related so the hybrids were classified into 75 groups with each group containing individual hybrids that showed similar patterns of Rogers distances across linkage groups. Correlations between hybrid-group performance and hybrid-group Rogers distances were calculated. A significant correlation was observed between whole genome-based Rogers distance and yield ( r = 0.42). This association is too weak to be of value for identifying superior hybrid combinations. One reason for the generally poor association between parental genetic diversity and yield may be that important QTLs influencing heterosis are located in particular chromosome regions and not distributed evenly over the genome. Variation in the sign and magnitude of correlations between Rogers distance and hybrid-group performance for particular linkage groups observed in this study support this hypothesis. The concept of using diversity on individual linkage groups to predict performance was explored. Using data from just two linkage groups 38% of the variation in hybrid performance for grain yield could be explained. A model combining phenotypic trait data and parental diversity on particular linkage groups explained 71% of the variation in grain yield and has potential for use in the selection of heterotic hybrids.     

Identifications of two different mechanisms for sorghum midge resistance through QTL mapping

Sorghum midge is the one of the most damaging insect pests of grain sorghum production worldwide. At least three different mechanisms are involved in midge resistance. The genetic bases of these mechanisms, however, are poorly understood. In this study, for the first time, quantitative trait loci associated with two of the mechanisms of midge resistance, antixenosis and antibiosis, were identified in an RI (recombinant inbred) population from the cross of sorghum lines ICSV745 x 90562. Two genetic regions located on separate linkage groups were found to be associated with antixenosis and explained 12% and 15%, respectively, of the total variation in egg numbers/spikelet laid in a cage experiment. One region was significantly associated with antibiosis and explained 34.5% of the variation of the difference of egg and pupal counts in the RI population. The identification of genes for different mechanisms of midge resistance will be particularly useful for exploring new sources of midge resistance and for gene pyramiding of different mechanisms for increased security in sorghum breeding through marker-assisted selection.     

DNA polymorphisms in grain sorghum (Sorghum bicolor (L.) Moench)

Molecular markers [random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP)] were used to determine the frequency of DNA polymorphism in grain sorghum (Sorghum bicolor (L.) Moench). Twenty-nine oligonucleotide primers were employed for RAPDs, generating a total of 262 DNA fragments, of which 145 were polymorphic in at least one pairwise comparison between 36 genotypes. Individual primers differed significantly in their ability to detect genetic polymorphism in the species. The overall frequency of polymorphisms was low with a mean frequency of 0.117 polymorphisms per RAPD band being obtained from all pairwise comparisons between genotypes, with maximum and minimum values of 0.212 and 0.039, respectively. Results from phenetic analysis of bandsharing data were consistent with current sub-specific groupings of the species, with clusters of Durra, Zerazera, Caud-Nig, Caud-Kaura and Caffrorum being discernible. The results also indicated that individuals of a similar taxonomic grouping but different geographic origin may be genetically less identical than previously considered. Similar frequencies of polymorphism to that obtained with RAPDs were obtained with RFLPs. Results from these experiments indicated that a high level of genetic uniformity exists within S. bicolor.     

Identification of genomic regions associated with stay green in sorghum by testing RILs in multiple environments

Stay green is an important drought resistance trait for sorghum production. QTLs for this trait with consistent effects across a set of environments would increase the efficiency of selection because of its relatively low heritability. One hundred and sixty recombinant inbreds, derived from a cross between QL39 and QL41, were used as a segregating population for genome mapping and stay green evaluation. Phenotypic data were collected in replicated field trials from five sites and in three growing seasons, and analysed by fitting appropriate models to account for spatial variability and to describe the genotype by environment interaction. Interval mapping and non-parametric mapping identified three regions, each in a separate linkage group, associated with stay green in more than one trial, and two regions in single trial. The regions on linkage groups B and I were both consistently identified from three trials. The multiple environment testing was very helpful for correctly identifying QTLs associated with the trait. The utilisation of molecular markers for stay green in sorghum breeding is also discussed. Received: 22 March 1999 / Accepted: 11 November 1999     

Substituted phenols as repellents for male Costelytra zealandica (Goleoptera: Scarabaeidae) in mating flights

Methyl‐ and halogen‐substituted phenols were found to be strongly repellent to male Costelytra zealandica (White) beetles in mating flights. Phenols substituted in the 2‐position were stronger repellents than those substituted in the 3‐ or 4‐position. Some of these compounds reduced the effectiveness of a potent sex attractant source by > 90 %.