Tissue-Specific Transcriptomic Profiling of Sorghum propinquum using a Rice Genome Array

Sorghum (Sorghum bicolor) is one of the world''s most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were expressed predominantly in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in Oryza longistaminata and S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development.     

Targeted mapping of quantitative trait locus regions for rhizomatousness in chromosome SBI-01 and analysis of overwintering in a Sorghum bicolor × S. propinquum population

While rhizome formation is intimately associated with perennialism and the derived benefit of sustainability, the introduction of this trait into temperate-zone adapted Sorghum cultivars requires precise knowledge of the genetics conditioning this trait in order to minimize the risk of weediness (e.g., Johnsongrass, S. halepense) while maximizing the productivity of perennial sorghum. As an incremental step towards dissecting the genetics of perennialism, a segregating F4 heterogeneous inbred family derived from a cross between S. bicolor and S. propinquum was phenotyped in both field and greenhouse environments for traits related to over-wintering and rhizome formation. An unseasonably cold winter in 2011 provided high selection pressure, and hence 74.8 % of the population did not survive. This severe selection pressure for cold tolerance allowed the resolution of two previously unidentified over-wintering quantitative trait locus (QTL) and more powerful correlation models than previously reported. Conflicting with previous reports, a maximum of 33 % of over-wintering variation could be explained by above-ground shoot formation from rhizomes; however, every over-wintering plant exhibited rhizome growth. Thus, while rhizome formation is required for over-wintering, other factors also determine survival in this interspecific population. The fine mapping of a previously reported rhizome QTL on sorghum chromosome SBI-01 was conducted by targeting this genomic region with additional simple sequence repeat markers. Fine mapping reduced the 2-LOD rhizome QTL interval from ~59 to ~14.5 Mb, which represents a 75 % reduction in physical distance and a 53 % reduction in the number of putative genes in the locus.     

Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye

Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens).     

Genetic analysis of vegetative branching in sorghum

Key message

We identified quantitative trait loci influencing plant architecture that may be valuable in breeding of optimized genotypes for sustainable food and/or cellulosic biomass production, and advancing resilience to changing climates.

Abstract

We describe a 3-year study to identify quantitative trait loci (QTLs) for vegetative branching of sorghum in a recombinant inbred line population of 161 genotypes derived from two morphologically distinct parents, S. bicolor × S. propinquum. We quantify vegetative branching based on morphological position and physiological status. Different sets of QTLs for different levels of branching were identified. QTLs discovered on chromosomes 1, 3, 7 and 8 affect multiple vegetative branching variables, suggesting that these regions may contain genes that control general axillary meristem initiation. Other regions that only influence one vegetative branching trait could contain genes that influence developmental processes contributing to divergent patterns of plant architecture. We investigate the relationship between vegetative branching patterns and dry biomass, and conclude that tillers with mature panicles and immature secondary branches each show consistent positive correlation with dry biomass. Among 19 branching-related genes from rice, eight sorghum homologs of seven rice genes are in syntenic blocks within branching-related QTL likelihood intervals. Five of these eight genes are within 700 kb of SNPs significantly associated with differences in branching in genome-wide association study of a diversity panel of 377 sorghum accessions, and three contain striking allelic variations between S. bicolor and S. propinquum that are likely to impact gene functions. Unraveling genetic determinants for vegetative branching may contribute to deterministic breeding of optimized genotypes for sustainable food and cellulosic biomass production in both optimal and marginal conditions, which are resilient to future climates that are more volatile and more stressful.     

Identification of bioconversion quantitative trait loci in the interspecific cross Sorghum bicolor × Sorghum propinquum

For lignocellulosic bioenergy to be economically viable, genetic improvements must be made in feedstock quality including both biomass total yield and conversion efficiency. Toward this goal, multiple studies have considered candidate genes and discovered quantitative trait loci (QTL) associated with total biomass accumulation and/or grain production in bioenergy grass species including maize and sorghum. However, very little research has been focused on genes associated with increased biomass conversion efficiency. In this study, Trichoderma viride fungal cellulase hydrolysis activity was measured for lignocellulosic biomass (leaf and stem tissue) obtained from individuals in a F₅ recombinant inbred Sorghum bicolor × Sorghum propinquum mapping population. A total of 49 QTLs (20 leaf, 29 stem) were associated with enzymatic conversion efficiency. Interestingly, six high-density QTL regions were identified in which four or more QTLs overlapped. In addition to enzymatic conversion efficiency QTLs, two QTLs were identified for biomass crystallinity index, a trait which has been shown to be inversely correlated with conversion efficiency in bioenergy grasses. The identification of these QTLs provides an important step toward identifying specific genes relevant to increasing conversion efficiency of bioenergy feedstocks. DNA markers linked to these QTLs could be useful in marker-assisted breeding programs aimed at increasing overall bioenergy yields concomitant with selection of high total biomass genotypes.     

Development of microsatellite markers targeting (GATA) n motifs in sorghum [Sorghum bicolor (L.) Moench]

Microsatellite markers targeting (GATA) _n motifs are known to be highly polymorphic. Genome-wide development of such markers has not been reported in sorghum. The main objective of this study was to identify Class I microsatellites with (GATA) _n motifs in the sorghum genome through in silico analysis and assess their potential as molecular markers. The study identified a total of 128 such motifs, of which 14, 16 and 98 motifs were present in the genic, upstream and non-genic regions, respectively. The majority of the (GATA) _n motifs were found in the non-genic regions of the genome while 23.44 % of them were found within the genes and upstream of genes. About 110 PCR-based markers were developed targeting these microsatellites and 50 of them distributed across the genome were validated in 24 diverse sorghum genotypes representing different racial groups. Thirty-eight markers were polymorphic, with average polymorphism information content value of 0.69, and the sorghum genotypes could be grouped into two major clusters. These markers with robust amplification combined with good allelic diversity represent a new set of microsatellite markers in sorghum reported for the first time that will be highly useful for various genetics and molecular breeding applications.