R. G. Henzell

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

Abstract 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.

Prediction of hybrid performance in grain sorghum using RFLP markers

Abstract.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 × 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.

Loss of genetic diversity associated with selection for resistance to sorghum midge in Australian sorghum

In recent years, hybrids with levels of resistance to sorghum midge (Stenodiplosis sorghicola Coquillett) have become available to Australian sorghum producers. These hybrids have been readily accepted to the extent that more than 80% of the sorghum growing area was planted to hybrids with some level of midge resistance by 1995. Since selection for resistance to sorghum midge is one of the primary objectives of Australian sorghum breeding programs, the relationship between resistance and genetic diversity was investigated.Genetic diversity and heterozygosity were assessed using restriction fragment length polymorphism analysis among 26 grain sorghum hybrids grown commercially in Australia.The genetic distances between each sorghum hybrid and a standard highly resistant hybrid were found to be strongly negatively correlated to hybrid midge resistance ratings (r = - 0.77, p < 0.001). In addition, the average heterozygosity of each hybrid was correlated with their midge resistance ratings (r = - 0.54, p < 0.01).The results indicate that the move to midge resistant hybrids has been associated with a narrowing of the genetic diversity and average heterozygosity of commercial sorghum hybrids. Repeated use of particular elite parent lines, linkage drag and genetic drift are likely to have contributed to this decline. This reduction in genetic diversity may have implications for the genetic vulnerability of sorghum in Australia and the rate of progress in breeding for yield.

Construction of a genetic map in a sorghum recombinant inbred line using probes from different sources and its comparison with other sorghum maps

A genetic map was established using 120 F-5 sorghum recombinant inbred lines (RILs) developed from a cross between 2 Australian elite sorghum inbred lines, QL39 and QL41. A variety of DNA probes, including sorghum genomic DNA, maize genomic DNA and cDNA, sugarcane genomic DNA and cDNA, and cereal anchor probes, were screened to identify DNA polymorphism between the parental lines. Using 5 restriction enzymes, probe polymorphism levels were low (26.5%). A total of 155 restriction fragment length polymorphism (RFLP) loci and 8 simple sequence repeat (SSR) loci were mapped onto 21 linkage groups, covering a map distance of approximately 1400 cM. Genes for 3 simply inherited traits, awns (AW), mesocarp thickness (Z), and organophosphate insecticide (OPR) reaction, were also mapped. The relationships between this map and other published sorghum maps were reviewed and a comparison of major sorghum RFLP maps attempted. This comparison is expected to enhance the effectiveness of existing mapping information and will facilitate efforts to map agronomically important traits in sorghum.

Identification of genomic regions for rust resistance in sorghum.

The location and effects of genomic regions for rust resistance in sorghum were determined. One hundred and sixty recombinant inbreds, which derived from a cross between QL39 and QL41, were used as a segregating population for genome mapping and rust resistance evaluation. Phenotypic data were collected in replicated field trials in two years. Interval mapping and non-parametric mapping identified four regions, each in a separate linkage group, associated with rust resistance. The region with the largest effect on rust resistance is on linkage group 10; it accounted for 40% of the total phenotypic variation.

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.

Mapping and characterization of Rf5: 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, Rf5, 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 Rf5, to a more normalized distribution reflecting the action of Rf5 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 Rf5, 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 Rf5 in A1 cytoplasm. In examining the genomic regions spanning the Rf5 locus, a cluster of pentatricopeptide gene family members with high homology to rice Rf1 and sorghum Rf2 were identified as potential candidates encoding Rf5.

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.

Host-plant resistance and biopesticides: ingredients for successful integrated pest management (IPM) in Australian sorghum production

There are two major pests of sorghum in Australia, the sorghum midge, Stenodiplosis sorghicola (Coquillett), and the corn earworm, Helicoverpa armigera (Hubner). During the past 10 years the management of these pests has undergone a revolution, due principally to the development of sorghum hybrids with resistance to sorghum midge. Also contributing has been the adoption of a nucleopolyhedrovirus for the management of corn earworm. The practical application of these developments has led to a massive reduction in the use of synthetic insecticides for the management of major pests of sorghum in Australia. These changes have produced immediate economic, environmental and social benefits. Other flow-on benefits include providing flexibility in planting times, the maintenance of beneficial arthropods and utilisation of sorghum as a beneficial arthropod nursery, a reduction in midge populations and a reduction in insecticide resistance development in corn earworm. Future developments in sorghum pest management are discussed.