Domestication to Crop Improvement: Genetic Resources for Sorghum and Saccharum (Andropogoneae)

Background Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. Genetic Resources The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes

Accelerated domestication of Australian native grasses

Australia is home to 10% of the world’s 10,000 grass species (Figure 1) and yet none of the currently cultivated species are native to this continent. The potential of several of Australia’s native species to be domesticated as new cereal crops was recorded by botanists as early as 1895 [1]. The most limiting factor for the use of native grasses, as either pasture or grain crops, is their lower yields when compared to domesticated species. In the case of grain yield addressing the issue of shattering at maturity greatly improves a species potential to be harvested and hence commercially exploited. Microlaena stipoides has been selected as the primary target species for accelerated domestication because of its favourable agronomic and genetic traits. Microlaena’s perennial growth cycle increases its water use efficiency while reducing tillage, and hence soil erosion. Its predominantly cleistogamous (selfing) breeding system allows the development of stable breeding lines and additionally this species also exhibits opportunistic chasmogamous (outcrossing) breeding cycles [2]. This will allow for cross breeding to be utilised to introgress beneficial traits from mutant individuals. Broad natural variation within the species occurs within and between populations across a wide range of environmental conditions [3] and collected ecotypes show tolerances to drought, acid soils, salinity, shade, frost and low fertiliser compared to current cereal crops [4, 5]. Microlaena is a dual purpose crop which can be grazed for about 6-8 months of the year and then locked up to set seed for grain harvest after rainfall events in the spring. Its high fodder value is due to a combination of good palatability, high digestibility (up to 79%), substantial biomass production (4-12t/ha) depending on water and nitrogen availability [6]. With respect to grain production Microlaena already has a good plant architecture, reasonable grain yield (130-1137kg/ha), large grain size in some accessions [4] and a similar endosperm morphology to rice [7]

The polymerase chain reaction (PCR): General methods

The polymerase chain reaction (PCR) converts very low quantities of DNA into very high quantities and is the foundation of many specialized techniques of molecular biology. PCR utilizes components of the cellular machinery of mitotic cell division in vitro which respond predictably to user inputs. This chapter introduces the principles of PCR and discusses practical considerations from target sequence definition through to optimization and application

Genome walking

Genome walking is a method for determining the DNA sequence of unknown genomic regions flanking a region of known DNA sequence. The Genome walking has the potential to capture 6–7 kb of sequence in a single round. Ideal for identifying gene promoter regions where only the coding region. Genome walking also has significant utility for capturing homologous genes in new species when there are areas in the target gene with strong sequence conservation to the characterized species. The increasing use of next-generation sequencing technologies will see the principles of genome walking adapted to in silico methods. However, for smaller projects, PCR-based genome walking will remain an efficient method of characterizing unknown flanking sequence

Endosperm and starch granule morphology in wild cereal relatives

Australia\u27s native grass species contain a diverse array of wild cereal relatives which are adapted to a broader range of environmental conditions than current commercial cereals and may contain novel alleles which have utility in commercial production systems. Characterizing the available variation in endosperm morphology is one of the first steps towards in planta manipulation of endosperm by either the introgression of novel alleles or bioengineering cereal starch and protein. The endosperm of 19 crop wild relatives (CWR) was examined using scanning electron microscopy (SEM). Mature caryopses were fixed, dehydrated, critical-point dried and then snap fractured transversely through the grain. Wild relatives exhibited similar types of starch granules to that of their respective cultivated species, though in general the wild species retained a greater proportion of the endosperm cell wall at maturity. The two species examined with no closely related cultivated species exhibited a rice-like endosperm. Wild sorghum relatives exhibited an abundance of endosperm variations described as variations in starch granule size, shape and surface morphology, and the distribution of protein bodies. This is particularly important because the grain of Sorghum bicolor has inherently low starch and protein digestibility. These variations within the wild relatives of commercial cereals may provide novel sources of genetic diversity for future grain improvement programmes

An analysis of the variation in the waxy gene in Australian native grass species

Global cereal consumption is derived from just eight of the 650 different genera within the Poaceae family, even though this is probably the most diverse flowering plant family. Currently there are over 69 genera of grasses recognised as being native to Australia. These may provide a valuable genetic resource for cereal quality improvement programs in the future. Genetic diversity between representatives of the five sub-families of Australian native grasses was observed at both the nucleotide and amino acid level for the waxy gene. This gene encodes Granule Bound Starch Synthase 1 (GBSS1), a key enzyme of starch synthesis, which displays a high degree of conservation across a wide range of higher plants. Conserved areas of the gene were used for PCR amplification and sequencing of a short fragment of the gene, which was then used as a platform for species specific/gene specific primer design. The BD GenomeWalker™ Universal Kit allowed sequencing of the native cereals’ genomic DNA, both upstream and down of the gene specific primer sites. Sequence analysis of the waxy gene indicated that although Australian native species display some degree of similarity to the ortholog in their respective commercial relatives, significant sequence differences are evident. Further more, the observed single nucleotide polymorphisms and indels translated to variation in the amino acid sequence of the waxy gene in these native species. This data supports the hypothesis that Australian native grasses may provide a new source of genetic diversity for future grain improvement programs

A new niche cereal may offer on-farm diversification that mitigates risks associated with climate variability

An Australian native grass, Microlaena stipoides, has been targeted for accelerated domestication utilising a combination of mutation breeding and high throughput genomics. In its natural environment, ecotypes of M .stipoides have shown tolerances to a suite of Australia\u27s environmental challenges including drought, frost, shade, salinity and acid soil. M .stipoides is a perennial species with high water use efficiency and once established becomes a zero-till crop

Accelerated domestication of Australian grasses as new sustainable food and fodder crops

Global cereal production is sourced from approximately only 0.2% of the world’s grass (Poaceae) species. None of the currently domesticated species are native to Australia and are therefore not well adapted to our environment. Australia’s short agricultural history and geographic isolation provide a unique opportunity to mine the 1000 grass species naturalised to this continent for new fodder and cereal crop alternatives which are intrinsically adapted to Australia’s variable and changing climate. Advances in molecular genetics over recent decades have provided new insights into the process of domestication and the key genes which have been selected for, both actively and passively, to produce cultivated species. Microlaena stipoides, a distant relative of rice, is being used as a model species for accelerated domestication by harnessing its genetic variation from both natural and induced mutations. The abundance of cereal genomic data is a key resource and is utlilsed in conjunction with endonucleolytic mutation analysis by internal labelling (EMAIL) and large scale SNP analyses for breeding selection. Accelerated domestication of native species may help to ensure food security in a future of declining water availability and changing climate