Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum

Genetic dissection of root architecture in Ethiopian sorghum landraces

KEY MESSAGE

This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.

Integrating stay-green and PIN-FORMED genes: PIN-FORMED genes as potential targets for designing climate-resilient cereal ideotypes

Plant architecture modification (e.g. short-stature crops) is one of the key outcomes of modern crop breeding for high-yielding crop varieties. In cereals, delayed senescence, or stay-green, is an important trait that enables post-anthesis drought stress adaptation. Stay-green crops can prolong photosynthetic capacity during grain-filling period under post-anthesis drought stress, which is essential to ensure grain yield is not impacted under drought stress conditions. Although various stay-green quantitative trait loci have been identified in cereals, the underlying molecular mechanisms regulating stay-green remain elusive. Recent advances in various gene-editing technologies have provided avenues to fast-track crop improvement, such as the breeding of climate-resilient crops in the face of climate change. We present in this viewpoint the focus on using sorghum as the model cereal crop, to study PIN-FORMED (PIN) auxin efflux carriers as means to modulate plant architecture, and the potential to employ it as an adaptive strategy to address the environmental challenges posed by climate uncertainties.

Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding

Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.

Genomic architecture of leaf senescence in sorghum (Sorghum bicolor)

Leaf senescence in sorghum is primarily controlled by the progression, but not by the onset of senescence. The senescence-delaying haplotypes of 45 key genes accentuated from landraces to improved lines. Leaf senescence is a genetically programmed developmental process and plays a central role for plant survival and crop production by remobilising nutrients accumulated in senescent leaves. In theory, the ultimate outcome of leaf senescence is determined by the onset and progression of senescence, but how these two processes contribute to senescence is not fully illustrated in crops and the genetic basis for them is not well understood. Sorghum (Sorghum bicolor), which is known for the remarkable stay-green trait, is ideal for dissecting the genomic architecture underlying the regulation of senescence. In this study, a diverse panel of 333 sorghum lines was explored for the onset and progression of leaf senescence. Trait correlation analysis showed that the progression of leaf senescence, rather than the onset of leaf senescence, significantly correlated with variations of the final leaf greenness. This notion was further supported by GWAS, which identified 31 senescence-associated genomic regions containing 148 genes, of which 124 were related to the progression of leaf senescence. The senescence-delaying haplotypes of 45 key candidate genes were enriched in lines with extremely prolonged senescence duration, while senescence-promoting haplotypes in those with extremely accelerated senescence. Haplotype combinations of these genes could well explain the segregation of the senescence trait in a recombinant inbred population. We also demonstrated that senescence-delaying haplotypes of candidate genes were under strong selection during sorghum domestication and genetic improvement. Together, this research advanced our understanding of crop leaf senescence and provided a suite of candidate genes for functional genomics and molecular breeding.

Genetic modification of PIN genes induces causal mechanisms of stay-green drought adaptation phenotype

The stay-green trait is recognized as a key drought adaptation mechanism in cereals worldwide. Stay-green sorghum plants exhibit delayed senescence of leaves and stems, leading to prolonged growth, a reduced risk of lodging, and higher grain yield under end-of-season drought stress. More than 45 quantitative trait loci (QTL) associated with stay-green have been identified, including two major QTL (Stg1 and Stg2). However, the contributing genes that regulate functional stay-green are not known. Here we show that the PIN FORMED family of auxin efflux carrier genes induce some of the causal mechanisms driving the stay-green phenotype in sorghum, with SbPIN4 and SbPIN2 located in Stg1 and Stg2, respectively. We found that nine of 11 sorghum PIN genes aligned with known stay-green QTL. In transgenic studies, we demonstrated that PIN genes located within the Stg1 (SbPIN4), Stg2 (SbPIN2), and Stg3b (SbPIN1) QTL regions acted pleiotropically to modulate canopy development, root architecture, and panicle growth in sorghum, with SbPIN1, SbPIN2, and SbPIN4 differentially expressed in various organs relative to the non-stay-green control. The emergent consequence of such modifications in canopy and root architecture is a stay-green phenotype. Crop simulation modelling shows that the SbPIN2 phenotype can increase grain yield under drought.

Genome-wide association studies identify putative pleiotropic locus mediating drought tolerance in sorghum

Drought is a key constraint on plant productivity and threat to food security. Sorghum (Sorghum bicolor L. Moench), a global staple food and forage crop, is among the most drought-adapted cereal crops, but its adaptation is not yet well understood. This study aims to better understand the genetic basis of preflowering drought in sorghum and identify loci underlying variation in water use and yield components under drought. A panel of 219 diverse sorghum from West Africa was phenotyped for yield components and water use in an outdoor large-tube lysimeter system under well-watered (WW) versus a preflowering drought water-stressed (WS) treatment. The experimental system was validated based on characteristic drought response in international drought tolerant check genotypes and genome-wide association studies (GWAS) that mapped the major height locus at QHT7.1 and Dw3. GWAS further identified marker trait associations (MTAs) for drought-related traits (plant height, flowering time, forage biomass, grain weight, water use) that each explained 7-70% of phenotypic variance. Most MTAs for drought-related traits correspond to loci not previously reported, but some MTA for forage biomass and grain weight under WS co-localized with staygreen post-flowering drought tolerance loci (Stg3a and Stg4). A globally common allele at S7_50055849 is associated with several yield components under drought, suggesting that it tags a major pleiotropic variant controlling assimilate partitioning to grain versus vegetative biomass. The GWAS revealed oligogenic variants for drought tolerance in sorghum landraces, which could be used as trait predictive markers for improved drought adaptation.

Dissecting the genetic control of natural variation in sorghum photosynthetic response to drought stress

Drought stress causes crop yield losses worldwide. Sorghum is a C4 species tolerant to moderate drought stress, and its extensive natural variation for photosynthetic traits under water-limiting conditions can be exploited for developing cultivars with enhanced stress tolerance. The objective of this study was to discover genes/genomic regions that control the sorghum photosynthetic capacity under pre-anthesis water-limiting conditions. We performed a genome-wide association study for seven photosynthetic gas exchange and chlorophyll fluorescence traits during three periods of contrasting soil volumetric water content (VWC): control (30% VWC), drought (15% VWC), and recovery (30% VWC). Water stress was imposed with an automated irrigation system that generated a controlled dry-down period for all plants, to perform an unbiased genotypic comparison. A total of 60 genomic regions were associated with natural variation in one or more photosynthetic traits in a particular treatment or with derived variables. We identified 33 promising candidate genes with predicted functions related to stress signaling, oxidative stress protection, hormonal response to stress, and dehydration protection. Our results provide new knowledge about the natural variation and genetic control of sorghum photosynthetic response to drought with the ultimate goal of improving its adaptation and productivity under water stress scenarios.

Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize

Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.

Genetic control of source-sink relationships in grain sorghum

QTL hotspots identified for selected source-sink-related traits provide the opportunity for pyramiding favorable alleles for improving sorghum productivity under diverse environments. A sorghum bi-parental mapping population was evaluated under six different environments at Hays and Manhattan, Kansas, USA, in 2016 and 2017, to identify genomic regions controlling source-sink relationships. The population consisted of 210 recombinant inbred lines developed from US elite post-flowering drought susceptible (RTx430) and a known post-flowering drought tolerant cultivar (SC35). Selected physiological traits related to source (effective quantum yield of photosystem II and chlorophyll index), sink (grain yield per panicle) and panicle neck diameter were recorded during grain filling. The results showed strong phenotypic and genotypic association between panicle neck diameter and grain yield per panicle during mid-grain filling and at maturity. Multiple QTL model revealed 5-12 including 2-5 major QTL for each trait. Among them 3, 7 and 8 QTL for quantum yield, panicle neck diameter and chlorophyll index, respectively, have not been identified previously in sorghum. Phenotypic variation explained by QTL identified across target traits ranged between 5.5 and 25.4%. Panicle neck diameter and grain yield per panicle were positively associated, indicating the possibility of targeting common co-localized QTL to improve both traits simultaneously through marker-assisted selection. Three major QTL hotspots, controlling multiple traits were identified on chromosome 1 (52.23-61.18 Mb), 2 (2.52-11.43 Mb) and 3 (1.32-3.95 Mb). The identified genomic regions and underlying candidate genes can be utilized in pyramiding favorable alleles for improving source-sink relationships in sorghum under diverse environments.

Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress

Droughts negatively affect sorghum's productivity and nutritional quality. Across its diversity centers, however, there exist resilient genotypes that function differently under drought stress at various levels, including molecular and physiological. Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still significantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the effects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized findings on the effects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn affect seed filling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.

Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum

Although spikelet-related traits such as size of anther, spikelet, style, and stigma are associated with sexual reproduction in grasses, no QTLs have been reported in sorghum. Additionally, there are only a few reports on sorghum QTLs related to grain size, such as grain length, width, and thickness. In this study, we performed QTL analyses of nine spikelet-related traits (length of sessile spikelet, pedicellate spikelet, pedicel, anther, style, and stigma; width of sessile spikelet and stigma; and stigma pigmentation) and six grain-related traits (length, width, thickness, length/width ratio, length/thickness ratio, and width/thickness ratio) using sorghum recombinant inbred lines. We identified 36 and 7 QTLs for spikelet-related traits and grain-related traits, respectively, and found that most sorghum spikelet organ length- and width-related traits were partially controlled by the dwarf genes Dw1 and Dw3. Conversely, we found that these Dw genes were not strongly involved in the regulation of grain size. The QTLs identified in this study aid in understanding the genetic basis of spikelet- and grain-related traits in sorghum.

Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C4 rhizomatous grasses Miscanthus and switchgrass

Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter-binding protein-Like, MADS-box SEPELLATA2 and gibberellin-responsive bHLH137. The former is emerging as a key component of the age-related flowering time pathway.

Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size

Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.

Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals

Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype's genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome-wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC-NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype's capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.

Photosynthetic Metabolism under Stressful Growth Conditions as a Bases for Crop Breeding and Yield Improvement

Increased periods of water shortage and higher temperatures, together with a reduction in nutrient availability, have been proposed as major factors that negatively impact plant development. Photosynthetic CO2 assimilation is the basis of crop production for animal and human food, and for this reason, it has been selected as a primary target for crop phenotyping/breeding studies. Within this context, knowledge of the mechanisms involved in the response and acclimation of photosynthetic CO2 assimilation to multiple changing environmental conditions (including nutrients, water availability, and rising temperature) is a matter of great concern for the understanding of plant behavior under stress conditions, and for the development of new strategies and tools for enhancing plant growth in the future. The current review aims to analyze, from a multi-perspective approach (ranging across breeding, gas exchange, genomics, etc.) the impact of changing environmental conditions on the performance of the photosynthetic apparatus and, consequently, plant growth.

Genomic signatures of seed mass adaptation to global precipitation gradients in sorghum

Seed mass is a key component of adaptation in plants and a determinant of yield in crops. The climatic drivers and genomic basis of seed mass variation remain poorly understood. In the cereal crop Sorghum bicolor, globally-distributed landraces harbor abundant variation in seed mass, which is associated with precipitation in their agroclimatic zones of origin. This study aimed to test the hypothesis that diversifying selection across precipitation gradients, acting on ancestral cereal grain size regulators, underlies seed mass variation in global sorghum germplasm. We tested this hypothesis in a set of 1901 georeferenced and genotyped sorghum landraces, 100-seed mass from common gardens, and bioclimatic precipitation variables. As predicted, 100-seed mass in global germplasm varies significantly among botanical races and is correlated to proxies of the precipitation gradients. With general and mixed linear model genome-wide associations, we identified 29 and 56 of 100 a priori candidate seed size genes with polymorphisms in the top 1% of seed mass association, respectively. Eleven of these genes harbor polymorphisms associated with the precipitation gradient, including orthologs of genes that regulate seed size in other cereals. With FarmCPU, 13 significant SNPs were identified, including one at an a priori candidate gene. Finally, we identified eleven colocalized outlier SNPs associated with seed mass and precipitation that also carry signatures of selection based on F_ST scans and PCAdapt, which represents a significant enrichment. Our findings suggest that seed mass in sorghum was shaped by diversifying selection on drought stress, and can inform genomics-enabled breeding for climate-resilient cereals.

Genetic Architecture of domestication- and improvement-related traits using a population derived from Sorghum virgatum and Sorghum bicolor

The genetic basis of domestication and improvement remains largely unknown in sorghum as a typical multiple-origins species. In this study, the F₂ and F₃ populations derived from a cross between Sorghum virgatum and domesticated sorghum were used to study the genetic architecture of domestication- and improvement-related traits. We found that human selection had greatly reshaped sorghum through the Quantitative Trait Loci (QTLs) with large genetic effects in the traits of harvest, plant architecture and grain taste including the reduction of shattering, few branches, short plant stature and the removal of polyphenols from seed. The expansion of seed width was selected to improve the yield through accumulating small-effect QTLs. Two major QTLs of plant height (QTI-ph1 and dw1) were narrowed down into 24.5-kilobase (kb) and 13.9-kb, respectively. DNA diversity analysis and association mapping of dw1 gene suggested the functional variant (A1361 T) might originate from the same event not long time ago. Our results supported that parallel phenotypic changes across different species during domestication and improvement might share the same genetic basis, QTL × QTL interactions might not play an important role in the reshaping of traits during sorghum domestication and improvement, and offered new views on transgressive segregation and segregation distortion. Our study greatly deepens our understandings of the genetic basis of sorghum domestication and improvement.

Unraveling the genetic complexity underlying sorghum response to water availability

Understanding the adaptation mechanisms of sorghum to drought and the underlying genetic architecture may help to improve its production in a wide range of environments. By crossing a high yielding parent (HYP) and a drought tolerant parent (DTP), we obtained 140 recombinant inbred lines (RILs), which were genotyped with 120 DArT and SSR markers covering 14 linkage groups (LGs). A subset of 100 RILs was evaluated three times in control and drought treatments to genetically dissect their response to water availability. Plants with early heading date (HD) in the drought treatment maintained yield (YLD) level by reducing seed number SN and increasing hundred seed weight (HSW). In contrast, early HD in the control treatment increased SN, HSW and YLD. In total, 133 significant QTL associated with the measured traits were detected in ten hotspot regions. Antagonistic, pleiotropic effects of a QTL cluster mapped on LG-6 may explain the observed trade-offs between SN and HSW: Alleles from DTP reduced SN and the alleles from HYP increased HSW under drought stress, but not in the control treatment. Our results illustrate the importance of considering genetic and environmental factors in QTL mapping to better understand plant responses to drought and to improve breeding programs.

Stay-Green QTLs Response in Adaptation to Post-Flowering Drought Depends on the Drought Severity

Stay-green trait enhances sorghum adaptation to post-flowering drought. Six stay-green backcross introgression lines (BILs) carrying one or more stay-green QTLs (Stg1-4) and their parents were characterized under non-stress (W100: 100% of soil field capacity (FC)) and two levels of post-flowering drought (W75: 75% FC; W50: 50% FC) in a controlled condition. We aimed to study the response and identify the drought threshold of these QTLs under different levels of post-flowering drought and find traits closely contributing to grain yield (GY) under different drought severity. W50 caused the highest reduction in BILs performance. From W100 to W50, the GY of the recurrent parent reduced by 70%, whereas that of the BILs reduced by only 36%. W75 and W50 induce different behavior/response compared to W100. Harvest index contributed to the GY under the three water regimes. For high GY under drought transpiration rate at the beginning of drought and mid-grain filling was important at W75, whereas it was important at mid-grain filling and late-grain filling at W50. Stay-green trait can be scored simply with the relative number of green leaves/plants under both irrigated and stress environments. QTL pyramiding might not always be necessary to stabilize or increase the GY under post-flowering drought. The stay-green QTLs increase GY under drought by manipulating water utilization depending on drought severity.

Sorghum stem aerenchyma formation is regulated by SbNAC_D during internode development

Sorghum bicolor is a drought-resilient C4 grass used for production of grain, forage, sugar, and biomass. Sorghum genotypes capable of accumulating high levels of stem sucrose have solid stems that contain low levels of aerenchyma. The D-locus on SBI06 modulates the extent of aerenchyma formation in sorghum stems and leaf midribs. A QTL aligned with this locus was identified and fine-mapped in populations derived from BTx623*IS320c, BTx623*R07007, and BTx623*Standard broomcorn. Analysis of coding polymorphisms in the fine-mapped D-locus showed that genotypes that accumulate low levels of aerenchyma encode a truncated NAC transcription factor (Sobic.006G147400, SbNAC_d1), whereas parental lines that accumulate higher levels of stem aerenchyma encode full-length NAC TFs (SbNAC-D). During vegetative stem development, aerenchyma levels are low in nonelongated stem internodes, internode growing zones, and nodes. Aerenchyma levels increase in recently elongated internodes starting at the top of the internode near the center of the stem. SbNAC_D was expressed at low levels in nonelongated internodes and internode growing zones and at higher levels in regions of stem internodes that form aerenchyma. SbXCP1, a gene encoding a cysteine protease involved in programmed cell death, was induced in SbNAC_D genotypes in parallel with aerenchyma formation in sorghum stems but not in SbNAC_d1 genotypes. Several sweet sorghum genotypes encode the recessive SbNAC_d1 allele and have low levels of stem aerenchyma. Based on these results, we propose that SbNAC_D is the D-gene identified by Hilton (1916) and that allelic variation in SbNAC_D modulates the extent of aerenchyma formation in sorghum stems.

Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems

Pith parenchyma cells store water in various plant organs. These cells are especially important for producing sugar and ethanol from the sugar juice of grass stems. In many plants, the death of pith parenchyma cells reduces their stem water content. Previous studies proposed that a hypothetical D gene might be responsible for the death of stem pith parenchyma cells in Sorghum bicolor, a promising energy grass, although its identity and molecular function are unknown. Here, we identify the D gene and note that it is located on chromosome 6 in agreement with previous predictions. Sorghum varieties with a functional D allele had stems enriched with dry, dead pith parenchyma cells, whereas those with each of six independent nonfunctional D alleles had stems enriched with juicy, living pith parenchyma cells. D expression was spatiotemporally coupled with the appearance of dead, air-filled pith parenchyma cells in sorghum stems. Among D homologs that are present in flowering plants, Arabidopsis ANAC074 also is required for the death of stem pith parenchyma cells. D and ANAC074 encode previously uncharacterized NAC transcription factors and are sufficient to ectopically induce programmed death of Arabidopsis culture cells via the activation of autolytic enzymes. Taken together, these results indicate that D and its Arabidopsis ortholog, ANAC074, are master transcriptional switches that induce programmed death of stem pith parenchyma cells. Thus, targeting the D gene will provide an approach to breeding crops for sugar and ethanol production.

Genotyping by Sequencing of 393 Sorghum bicolor BTx623 × IS3620C Recombinant Inbred Lines Improves Sensitivity and Resolution of QTL Detection

We describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)-based SNP markers in a F₆-F₈ recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTL relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTL for each trait and provide evidence against pleiotropy. Ten non- random syntenic regions conferring QTL for the same trait suggest that those QTL may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTL for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.

Sorghum Landrace Collections from Cooler Regions of the World Exhibit Magnificent Genetic Differentiation and Early Season Cold Tolerance

Cold temperature is an important abiotic stress affecting sorghum production in temperate regions. It reduces seed germination, seedling emergence and seedling vigor thus limiting the production of the crop both temporally and spatially. The objectives of this study were (1) to assess early season cold temperature stress response of sorghum germplasm from cooler environments and identify sources of tolerance for use in breeding programs, (2) to determine population structure and marker-trait association among these germplasms for eventual development of marker tools for improving cold tolerance. A total of 136 sorghum accessions from cooler regions of the world were phenotyped for seedling growth characteristics under cold temperature imposed through early planting. The accessions were genotyped using 67 simple sequence repeats markers spanning all ten linkage groups of sorghum, of which 50 highly polymorphic markers were used in the analysis. Genetic diversity and population structure analyses sorted the population into four subpopulations. Several accessions distributed in all subpopulations showed either better or comparable level of tolerance to the standard cold tolerance source, Shan qui red. Association analysis between the markers and seedling traits identified markers Xtxp34, Xtxp88, and Xtxp319 as associated with seedling emergence, Xtxp211 and Xtxp304 with seedling dry weight, and Xtxp20 with seedling height. The markers were detected on chromosomes previously found to harbor QTLs associated with cold tolerance in sorghum. Once validated these may serve as genomic tools in marker-assisted breeding or for screening larger pool of genotypes to identify additional sources of cold tolerance.

Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus

Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) "835" and "B2," including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69-12.6 of the LOD value, and 0.82-16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs.

Quantitative genetic analysis of agronomic and morphological traits in sorghum, Sorghum bicolor

The productivity in sorghum is low, owing to various biotic and abiotic constraints. Combining insect resistance with desirable agronomic and morphological traits is important to increase sorghum productivity. Therefore, it is important to understand the variability for various agronomic traits, their heritabilities and nature of gene action to develop appropriate strategies for crop improvement. Therefore, a full diallel set of 10 parents and their 90 crosses including reciprocals were evaluated in replicated trials during the 2013-14 rainy and postrainy seasons. The crosses between the parents with early- and late-flowering flowered early, indicating dominance of earliness for anthesis in the test material used. Association between the shoot fly resistance, morphological, and agronomic traits suggested complex interactions between shoot fly resistance and morphological traits. Significance of the mean sum of squares for GCA (general combining ability) and SCA (specific combining ability) of all the studied traits suggested the importance of both additive and non-additive components in inheritance of these traits. The GCA/SCA, and the predictability ratios indicated predominance of additive gene effects for majority of the traits studied. High broad-sense and narrow-sense heritability estimates were observed for most of the morphological and agronomic traits. The significance of reciprocal combining ability effects for days to 50% flowering, plant height and 100 seed weight, suggested maternal effects for inheritance of these traits. Plant height and grain yield across seasons, days to 50% flowering, inflorescence exsertion, and panicle shape in the postrainy season showed greater specific combining ability variance, indicating the predominance of non-additive type of gene action/epistatic interactions in controlling the expression of these traits. Additive gene action in the rainy season, and dominance in the postrainy season for days to 50% flowering and plant height suggested G X E interactions for these traits.

Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis

Heterosis is a main contributor to yield increase in many crop species. Different mechanisms have been proposed for heterosis: dominance, overdominance, epistasis, epigenetics, and protein metabolite changes. However, only limited examples of molecular dissection and validation of these mechanisms are available. Here, we present an example of discovery and validation of heterosis generated by a combination of repulsion linkage and dominance. Using a recombinant inbred line population, a separate quantitative trait locus (QTL) for plant height (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 gene. With two loci having repulsion linkage between two inbreds, heterosis in the hybrid can appear as a single locus with an overdominance mode of inheritance (i.e., pseudo-overdominance). Individually, alleles conferring taller plant height exhibited complete dominance over alleles conferring shorter height. Detailed analyses of different height components demonstrated that qHT7.1 affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. Computer simulations show that repulsion linkage could influence QTL detection and estimation of effect in segregating populations. Guided by findings in linkage mapping, a genome-wide association study of plant height with a sorghum diversity panel pinpointed genomic regions underlying the trait variation, including Dw1, Dw2, Dw3, Dw4, and qHT7.1. Multilocus mixed model analysis confirmed the advantage of complex trait dissection using an integrated approach. Besides identifying a specific genetic example of heterosis, our research indicated that integrated molecular dissection of complex traits in different population types can enable plant breeders to fine tune the breeding process for crop production.

Fine mapping of qGW1, a major QTL for grain weight in sorghum

We detected seven QTLs for 100-grain weight in sorghum using an F 2 population, and delimited qGW1 to a 101-kb region on the short arm of chromosome 1, which contained 13 putative genes. Sorghum is one of the most important cereal crops. Breeding high-yielding sorghum varieties will have a profound impact on global food security. Grain weight is an important component of grain yield. It is a quantitative trait controlled by multiple quantitative trait loci (QTLs); however, the genetic basis of grain weight in sorghum is not well understood. In the present study, using an F2 population derived from a cross between the grain sorghum variety SA2313 (Sorghum bicolor) and the Sudan-grass variety Hiro-1 (S. bicolor), we detected seven QTLs for 100-grain weight. One of them, qGW1, was detected consistently over 2 years and contributed between 20 and 40 % of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants from a fine-mapping F3 population, we delimited qGW1 to a 101-kb region on the short arm of chromosome 1, containing 13 predicted gene models, one of which was found to be under purifying selection during domestication. However, none of the grain size candidate genes shared sequence similarity with previously cloned grain weight-related genes from rice. This study will facilitate isolation of the gene underlying qGW1 and advance our understanding of the regulatory mechanisms of grain weight. SSR markers linked to the qGW1 locus can be used for improving sorghum grain yield through marker-assisted selection.

Stability and genetic control of morphological, biomass and biofuel traits under temperate maritime and continental conditions in sweet sorghum (Sorghum bicolour)

Eight morphological, biomass and biofuel traits were found with high broad-sense heritability and 18 significant QTLs discovered including one locus controlling the stem juice trait for sorghum grown in Denmark and China. Sweet sorghum with tall plant, fast maturation and high stem Brix content can be bred as a biofuel crop for Northern Europe. Sweet sorghum (Sorghum bicolour), a native tropical C4 crop, has attracted interest as a bioenergy crop in northern countries due to its juice-rich stem and high biomass production. Little is known about the traits important for its adaptation to high altitude climatic conditions and their genetic controls. Recombinant inbred lines derived from a cross between a sweet and a grain kaoliang sorghum were used in five field trials in Denmark and in China to identify the stability and genetic controls of morphological, biomass and biofuel traits during three consecutive summers with short duration, cool temperatures and long days. Eight out of 15 traits were found with high broad-sense heritability. Strong positive correlations between plant height and biomass traits were observed, while Brix and juice content were under different genetic controls. Using newly developed PAV (presence and absence variant) markers, 53 QTLs were detected, of which 18 were common for both countries, including a locus controlling stem juice (LOD score = 20.5, r (2) = 37.5 %). In Denmark, the heading stage correlated significantly with biomass and morphology traits, and two significant maturity QTLs detected on chromosomes SBI01 and SBI02 co-localised with QTLs previously associated with early-stage chilling tolerance, suggesting that accelerating maturation might be a means of coping with low-temperature stress. Our results suggest that selection for tall and fast maturating sorghum plants combined with high Brix content represents a high potential for breeding bioenergy crop for Northern Europe.

Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)

BACKGROUND

Domestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice.

RESULTS

We performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved 'hotspots' in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum.

CONCLUSIONS

Intersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.

Comparative Genetics of Seed Size Traits in Divergent Cereal Lineages Represented by Sorghum (Panicoidae) and Rice (Oryzoidae)

Seed size is closely related to fitness of wild plants, and its modification has been a key recurring element in domestication of seed/grain crops. In sorghum, a genomic and morphological model for panicoid cereals, a rich history of research into the genetics of seed size is reflected by a total of 13 likelihood intervals determined by conventional QTL (linkage) mapping in 11 nonoverlapping regions of the genome. To complement QTL data and investigate whether the discovery of seed size QTL is approaching “saturation,” we compared QTL data to GWAS for seed mass, seed length, and seed width studied in 354 accessions from a sorghum association panel (SAP) that have been genotyped at 265,487 SNPs. We identified nine independent GWAS-based “hotspots” for seed size associations. Targeted resequencing near four association peaks with the most notable linkage disequilibrium provides further support of the role(s) of these regions in the genetic control of sorghum seed size and identifies two candidate causal variants with nonsynonymous mutations. Of nine GWAS hotspots in sorghum, seven have significant correspondence with rice QTL intervals and known genes for components of seed size on orthologous chromosomes. Identifying intersections between positional and association genetic data are a potentially powerful means to mitigate constraints associated with each approach, and nonrandom correspondence of sorghum (panicoid) GWAS signals to rice (oryzoid) QTL adds a new dimension to the ability to leverage genetic data about this important trait across divergent plants.

Two distinct classes of QTL determine rust resistance in sorghum

BACKGROUND

Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments.

RESULTS

In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust.

CONCLUSIONS

The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.

Drought adaptation of stay-green sorghum is associated with canopy development, leaf anatomy, root growth, and water uptake

Stay-green sorghum plants exhibit greener leaves and stems during the grain-filling period under water-limited conditions compared with their senescent counterparts, resulting in increased grain yield, grain mass, and lodging resistance. Stay-green has been mapped to a number of key chromosomal regions, including Stg1, Stg2, Stg3, and Stg4, but the functions of these individual quantitative trait loci (QTLs) remain unclear. The objective of this study was to show how positive effects of Stg QTLs on grain yield under drought can be explained as emergent consequences of their effects on temporal and spatial water-use patterns that result from changes in leaf-area dynamics. A set of four Stg near-isogenic lines (NILs) and their recurrent parent were grown in a range of field and semicontrolled experiments in southeast Queensland, Australia. These studies showed that the four Stg QTLs regulate canopy size by: (1) reducing tillering via increased size of lower leaves, (2) constraining the size of the upper leaves; and (3) in some cases, decreasing the number of leaves per culm. In addition, they variously affect leaf anatomy and root growth. The multiple pathways by which Stg QTLs modulate canopy development can result in considerable developmental plasticity. The reduction in canopy size associated with Stg QTLs reduced pre-flowering water demand, thereby increasing water availability during grain filling and, ultimately, grain yield. The generic physiological mechanisms underlying the stay-green trait suggest that similar Stg QTLs could enhance post-anthesis drought adaptation in other major cereals such as maize, wheat, and rice.

Detection and validation of stay-green QTL in post-rainy sorghum involving widely adapted cultivar, M35-1 and a popular stay-green genotype B35

BACKGROUND

Sorghum [Sorghum bicolor (L.) Moench] is an important dry-land cereal of the world providing food, fodder, feed and fuel. Stay-green (delayed-leaf senescence) is a key attribute in sorghum determining its adaptation to terminal drought stress. The objective of this study was to validate sorghum stay-green quantitative trait loci (QTL) identified in the past, and to identify new QTL in the genetic background of a post-rainy adapted genotype M35-1.

RESULTS

A genetic linkage map based on 245 F9 Recombinant Inbred Lines (RILs) derived from a cross between M35-1 (more senescent) and B35 (less senescent) with 237 markers consisting of 174 genomic, 60 genic and 3 morphological markers was used. The phenotypic data collected for three consecutive post-rainy crop seasons on the RIL population (M35-1 × B35) was used for QTL analysis. Sixty-one QTL were identified for various measures of stay-green trait and each trait was controlled by one to ten QTL. The phenotypic variation explained by each QTL ranged from 3.8 to 18.7%. Co-localization of QTL for more than five traits was observed on two linkage groups i.e. on SBI-09-3 flanked by S18 and Xgap206 markers and, on SBI-03 flanked by XnhsbSFCILP67 and Xtxp31. QTL identified in this study were stable across environments and corresponded to sorghum stay-green and grain yield QTL reported previously. Of the 60 genic SSRs mapped, 14 were closely linked with QTL for ten traits. A genic marker, XnhsbSFCILP67 (Sb03g028240) encoding Indole-3-acetic acid-amido synthetase GH3.5, was co-located with QTL for GLB, GLM, PGLM and GLAM on SBI-03. Genes underlying key enzymes of chlorophyll metabolism were also found in the stay-green QTL regions.

CONCLUSIONS

We validated important stay-green QTL reported in the past in sorghum and detected new QTL influencing the stay-green related traits consistently. Stg2, Stg3 and StgB were prominent in their expression. Collectively, the QTL/markers identified are likely candidates for subsequent verification for their involvement in stay-green phenotype using NILs and to develop drought tolerant sorghum varieties through marker-assisted breeding for terminal drought tolerance in sorghum.

Quantitative trait locus mapping of the transpiration ratio related to preflowering drought tolerance in sorghum (Sorghum bicolor)

To meet future food needs, grain production must increase despite reduced water availability, so waterproductivity must rise. One way to do this is to raise the ratio of biomass produced to water transpired, which is controlled by the ratio of CO2 assimilation (A) to transpiration (E) (i.e. the transpiration ratio, A : E divided by vapour pressure deficit) or anything affecting stomatal movement.. We describe the genetic variation and basis of A, E and A : E among 70 recombinant inbred lines (RILs) of sorghum (Sorghum bicolor (L.) Moench), using greenhouse experiments. Experiment 1 used 40% and 80% of field capacity (FC) as water regimes; Experiment 2 used 80% FC. Genotype had a significant effect on A, E and A : E. In Experiment 1, mean values for A : E were 1.2-4.4 mmol CO2 mol-1 H2O kPa-1 and 1.6-3.1 mmol CO2 mol-1 H2O kPa-1 under 40% and 80% FC, respectively. In Experiment 2, values were 5.6-9.8 mmol CO2 mol-1 H2O kPa-1. Pooled data for A : E and A : E VPD-1 from Experiment 1 indicate that A : E fell quickly at temperatures >32.3°C. A : E distributions were skewed. Mean heritabilities for A : E were 0.9 (40% FC) and 0.8 (80% FC). Three significant quantitative trait loci (QTLs) associated with A:E, two on SBI-09 and one on SBI-10, accounted for 17-21% of the phenotypic variation. Subsequent experiments identified 38 QTLs controlling variation in height, flowering, biomass, leaf area, greenness and stomatal density. Colocalisation of A : E QTLs with agronomic traits indicated that these QTLs can be used for improving sorghum performance through marker assisted selection (MAS) under preflowering drought stress.

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.

Population genetics structure of glyphosate-resistant Johnsongrass (Sorghum halepense L. Pers) does not support a single origin of the resistance

Single sequence repeats (SSR) developed for Sorghum bicolor were used to characterize the genetic distance of 46 different Sorghum halepense (Johnsongrass) accessions from Argentina some of which have evolved toward glyphosate resistance. Since Johnsongrass is an allotetraploid and only one subgenome is homologous to cultivated sorghum, some SSR loci amplified up to two alleles while others (presumably more conserved loci) amplified up to four alleles. Twelve SSR providing information of 24 loci representative of Johnsongrass genome were selected for genetic distance characterization. All of them were highly polymorphic, which was evidenced by the number of different alleles found in the samples studied, in some of them up to 20. UPGMA and Mantel analysis showed that Johnsongrass glyphosate-resistant accessions that belong to different geographic regions do not share similar genetic backgrounds. In contrast, they show closer similarity to their neighboring susceptible counterparts. Discriminant Analysis of Principal Components using the clusters identified by K-means support the lack of a clear pattern of association among samples and resistance status or province of origin. Consequently, these results do not support a single genetic origin of glyphosate resistance. Nucleotide sequencing of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) encoding gene from glyphosate-resistant and susceptible accessions collected from different geographic origins showed that none presented expected mutations in aminoacid positions 101 and 106 which are diagnostic of target-site resistance mechanism.

Mapping QTL for grain yield and other agronomic traits in post-rainy sorghum [Sorghum bicolor (L.) Moench]

Sorghum, a cereal of economic importance ensures food and fodder security for millions of rural families in the semi-arid tropics. The objective of the present study was to identify and validate quantitative trait loci (QTL) for grain yield and other agronomic traits using replicated phenotypic data sets from three post-rainy dry sorghum crop seasons involving a mapping population with 245 F9 recombinant inbred lines derived from a cross of M35-1 × B35. A genetic linkage map was constructed with 237 markers consisting of 174 genomic, 60 genic and 3 morphological markers. The QTL analysis for 11 traits following composite interval mapping identified 91 QTL with 5-12 QTL for each trait. QTL detected in the population individually explained phenotypic variation between 2.5 and 30.3 % for a given trait and six major genomic regions with QTL effect on multiple traits were identified. Stable QTL across seasons were identified. Of the 60 genic markers mapped, 21 were found at QTL peak or tightly linked with QTL. A gene-based marker XnhsbSFCILP67 (Sb03g028240) on SBI-03, encoding indole-3-acetic acid-amido synthetase GH3.5, was found to be involved in QTL for seven traits. The QTL-linked markers identified for 11 agronomic traits may assist in fine mapping, map-based gene isolation and also for improving post-rainy sorghum through marker-assisted breeding.

Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection

Plant height and maturity are two critical traits in sorghum breeding. To develop molecular tools and to identify genes underlying the traits for molecular breeding, we developed 14,739 SNP markers used to genotype the complete sorghum [Sorghum bicolor (L.) Moench] mini core collection. The collection was evaluated in four rainy and three post-rainy season environments for plant height and maturity. Association analysis identified six marker loci linked to height and ten to maturity in at least two environments with at least two SNPs in each locus. Of these, 14 were in close proximity to previously mapped height/maturity QTL in sorghum. Candidate genes for maturity or plant height close to the marker loci include a sugar transporter (SbSUC9), an auxin response factor (SbARF3), an FLC and FT regulator (SbMED12), and a photoperiod response gene (SbPPR1) for maturity and peroxidase 53, and an auxin transporter (SbLAX4) for plant height. Linkage disequilibrium analysis showed that SbPPR1 and SbARF3 were in regions with reduced sequence variation among early-maturing accessions, suggestive of past purifying selection. We also found a linkage disequilibrium block that existed only among the accessions with short plant height in rainy season environments. The block contains a gene homologous to the Arabidopsis flowering time gene, LUMINIDEPENDENS (LD). Functional LD promotes early maturity while mutation delays maturity, affecting plant height. Previous studies also found reduced sequence variations within this gene. These newly-mapped SNP markers will facilitate further efforts to identify plant height or maturity genes in sorghum.

Molecular mapping of genomic regions harbouring QTLs for root and yield traits in sorghum (Sorghum bicolor L. Moench)

Root system is a vital part of plants for absorbing soil moisture and nutrients and it influences the drought tolerance. Identification of the genomic regions harbouring quantitative trait loci (QTLs) for root and yield traits, and the linked markers can facilitate sorghum improvement through marker-assisted selection (MAS) besides the deeper understanding of the plant response to drought stress. A population of 184 recombinant inbred lines (RILs), derived from E36-1 × SPV570, along with parents were phenotyped for component traits of yield in field and root traits in an above ground rhizotron. High estimates of heritability and genetic advance for all the root traits and for most of the yield traits, presents high scope for improvement of these traits by simple selection. A linkage map constructed with 104 marker loci comprising 50 EST-SSRs, 34 non-genic nuclear SSRs and 20 SNPs, and QTL analysis was performed using composite interval mapping (CIM) approach. A total of eight and 20 QTLs were mapped for root and yield related traits respectively. The QTLs for root volume, root fresh weight and root dry weight were found co-localized on SBI-04, supported by a positive correlation among these traits. Hence, these traits can be improved using the same linked markers. The lack of overlap between the QTLs of component traits of root and yield suggested that these two sets of parameters are independent in their influence and the possibility of combining these two traits might enhance productivity of sorghum under receding moisture condition.

Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time

Nested association mapping (NAM) offers power to dissect complex, quantitative traits. This study made use of a recently developed sorghum backcross (BC)-NAM population to dissect the genetic architecture of flowering time in sorghum; to compare the QTL identified with other genomic regions identified in previous sorghum and maize flowering time studies and to highlight the implications of our findings for plant breeding. A subset of the sorghum BC-NAM population consisting of over 1,300 individuals from 24 families was evaluated for flowering time across multiple environments. Two QTL analysis methodologies were used to identify 40 QTLs with predominately small, additive effects on flowering time; 24 of these co-located with previously identified QTL for flowering time in sorghum and 16 were novel in sorghum. Significant synteny was also detected with the QTL for flowering time detected in a comparable NAM resource recently developed for maize (Zea mays) by Buckler et al. (Science 325:714-718, 2009). The use of the sorghum BC-NAM population allowed us to catalogue allelic variants at a maximal number of QTL and understand their contribution to the flowering time phenotype and distribution across diverse germplasm. The successful demonstration of the power of the sorghum BC-NAM population is exemplified not only by correspondence of QTL previously identified in sorghum, but also by correspondence of QTL in different taxa, specifically maize in this case. The unification across taxa of the candidate genes influencing complex traits, such as flowering time can further facilitate the detailed dissection of the genetic control and causal genes.

Genetic dissection of the temperature dependent emergence processes in sorghum using a cumulative emergence model and stability parameters

Among the major limitations for cultivating biomass sorghum in temperate regions is low temperature in spring that results in low and non-uniform emergence. The adaptation of sorghum to tropical and subtropical highlands gives hint of genetic variation in cold tolerance during emergence. The objective of the present study was to detect marker-trait associations for parameters describing the emergence process under different temperature regimes. A diversity set comprising 194 genotypes was tested in nine controlled environments with temperatures ranging from 9.4 to 19.9 °C. The genotypes were fingerprinted with 171 DArT markers. A piecewise linear regression model carried out on cumulative emergence was used to estimate genotype mean performance across environments and to carry out stability analysis on the parameters of the regression model. Base temperature (T (b)) and thermal time required for emergence (E (TS)) were determined based on median time to emergence data. Identified QTL positions were compared to marker-trait associations for final emergence percentages under low (FEP(cold)) and normal (FEP(normal)) temperatures. QTL for mean final emergence percentage (FEP), FEP(cold) and FEP(normal,) T (b) and E (TS) were detected on SBI-01. Other QTL-rich regions were located on SBI-03, SBI-04, SBI-06, SBI-08, and SBI-09. Marker-trait associations for T (b) and E (TS) co-localized to QTL for the across environment stability of FEP and the median time to emergence or emergence rate, respectively. We conclude that genome regions on six chromosomes highly influencing cold tolerance during emergence are promising for regional association studies and for the development of stable markers for marker-assisted selection.

Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits

For lignocellulosic bioenergy to become a viable alternative to traditional energy production methods, rapid increases in conversion efficiency and biomass yield must be achieved. Increased productivity in bioenergy production can be achieved through concomitant gains in processing efficiency as well as genetic improvement of feedstock that have the potential for bioenergy production at an industrial scale. The purpose of this review is to explore the genetic and genomic resource landscape for the improvement of a specific bioenergy feedstock group, the C4 bioenergy grasses. First, bioenergy grass feedstock traits relevant to biochemical conversion are examined. Then we outline genetic resources available bioenergy grasses for mapping bioenergy traits to DNA markers and genes. This is followed by a discussion of genomic tools and how they can be applied to understanding bioenergy grass feedstock trait genetic mechanisms leading to further improvement opportunities.

Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods

The productivity of sorghum is mainly determined by agronomically important traits. The genetic bases of these traits have historically been dissected and analysed through quantitative trait locus (QTL) mapping based on linkage maps with low-throughput molecular markers, which is one of the factors that hinder precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, an ultra-high-density linkage map based on high-quality single nucleotide polymorphisms (SNPs) generated from low-coverage sequences (~0.07 genome sequence) in a sorghum recombinant inbred line (RIL) population was constructed through new sequencing technology. This map consisted of 3418 bin markers and spanned 1591.4 cM of genome size with an average distance of 0.5 cM between adjacent bins. QTL analysis was performed and a total of 57 major QTLs were detected for eight agronomically important traits under two contrasting photoperiods. The phenotypic variation explained by individual QTLs varied from 3.40% to 33.82%. The high accuracy and quality of this map was evidenced by the finding that genes underlying two cloned QTLs, Dw3 for plant height (chromosome 7) and Ma1 for flowering time (chromosome 6), were localized to the correct genomic regions. The close associations between two genomic regions on chromosomes 6 and 7 with multiple traits suggested the existence of pleiotropy or tight linkage. Several major QTLs for heading date, plant height, numbers of nodes, stem diameter, panicle neck length, and flag leaf width were detected consistently under both photoperiods, providing useful information for understanding the genetic mechanisms of the agronomically important traits responsible for the change of photoperiod.

Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae)

Phenylalanine ammonia lyase (PAL) is the first entry enzyme of the phenylpropanoid pathway producing phenolics, widespread constituents of plant foods and beverages, including chlorogenic acids, polyphenols found at remarkably high levels in the coffee bean and long recognized as powerful antioxidants. To date, whereas PAL is generally encoded by a small gene family, only one gene has been characterized in Coffea canephora (CcPAL1), an economically important species of cultivated coffee. In this study, a molecular- and bioinformatic-based search for CcPAL1 paralogues resulted successfully in identifying two additional genes, CcPAL2 and CcPAL3, presenting similar genomic structures and encoding proteins with close sequences. Genetic mapping helped position each gene in three different coffee linkage groups, CcPAL2 in particular, located in a coffee genome linkage group (F) which is syntenic to a region of Tomato Chromosome 9 containing a PAL gene. These results, combined with a phylogenetic study, strongly suggest that CcPAL2 may be the ancestral gene of C. canephora. A quantitative gene expression analysis was also conducted in coffee tissues, showing that all genes are transcriptionally active, but they present distinct expression levels and patterns. We discovered that CcPAL2 transcripts appeared predominantly in flower, fruit pericarp and vegetative/lignifying tissues like roots and branches, whereas CcPAL1 and CcPAL3 were highly expressed in immature fruit. This is the first comprehensive study dedicated to PAL gene family characterization in coffee, allowing us to advance functional studies which are indispensable to learning to decipher what role this family plays in channeling the metabolism of coffee phenylpropanoids.

Mapping of QTLs underlying flowering time in sorghum [Sorghum bicolor (L.) Moench]

Due to its critical importance in crop yield, the photoperiodic regulation of flowering time is considered an important trait in sorghum breeding programs. In this study, quantitative trait loci for flowering time were detected using an F(2) population derived from a cross between Kikuchi Zairai, a late-flowering cultivar originating from Japan and SC112, an early-flowering cultivar originating from Ethiopia. F(2) plants were grown with their parents under a natural day length and a 12 h day length. Two linkage maps were constructed using 213 simple sequence repeats markers. Nine quantitative trait loci controlling flowering time were identified in F(2) plants grown under a natural day length, whereas 7 QTLs were identified under a 12 h day length. Five QTLs controlling flowering time were shared under both of the day length conditions.

Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences

Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.

QTL for nodal root angle in sorghum (Sorghum bicolor L. Moench) co-locate with QTL for traits associated with drought adaptation

Nodal root angle in sorghum influences vertical and horizontal root distribution in the soil profile and is thus relevant to drought adaptation. In this study, we report for the first time on the mapping of four QTL for nodal root angle (qRA) in sorghum, in addition to three QTL for root dry weight, two for shoot dry weight, and three for plant leaf area. Phenotyping was done at the six leaf stage for a mapping population (n = 141) developed by crossing two inbred sorghum lines with contrasting root angle. Nodal root angle QTL explained 58.2% of the phenotypic variance and were validated across a range of diverse inbred lines. Three of the four nodal root angle QTL showed homology to previously identified root angle QTL in rice and maize, whereas all four QTL co-located with previously identified QTL for stay-green in sorghum. A putative association between nodal root angle QTL and grain yield was identified through single marker analysis on field testing data from a subset of the mapping population grown in hybrid combination with three different tester lines. Furthermore, a putative association between nodal root angle QTL and stay-green was identified using data sets from selected sorghum nested association mapping populations segregating for root angle. The identification of nodal root angle QTL presents new opportunities for improving drought adaptation mechanisms via molecular breeding to manipulate a trait for which selection has previously been very difficult.