Identification of quantitative trait loci for resistance to shoot fly in sorghum [Sorghum bicolor (L.) Moench]

Realizing visionary goals for the International Year of Millet (IYoM): accelerating interventions through advances in molecular breeding and multiomics resources

MAIN CONCLUSION

Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential "nutricereal resource," aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as "Shree Anna," emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the "International Year of Millets (IYoM 2023)," emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences.

Multi-trait stability index for the identification of shoot fly (Atherigona soccata) resistant sorghum lines from a mini core collection

BACKGROUND

On sorghum, shoot fly (Atherigona soccata Rondani) is the most destructive insect pest causing enormous economic losses. Breeding for host plant resistance is the best and economically viable strategy to control shoot fly damage. For improving resistance, there is a need to identify better donors with resistance, stability and adaptability. Sorghum mini core set representing global genetic diversity offers opportunity to understand genetic diversity of resistance component traits, their genotype × year (G × Y), and to identify better donors based on mean performance of multiple shoot fly resistance traits coupled with stability.

RESULTS

Significant genetic variability and G × Y interaction was detected for all traits in the mini core set. Broad sense heritability and accuracy of selection for traits was high. Genetic correlation between deadhearts and leaf surface glossiness and with seedling height were negative while genetic correlation of deadhearts with oviposition was positive. The sorghum races did not establish any inherent relation with shoot fly resistance. Based on multiple trait stability index (MTSI), the study identified 12 stable resistant accessions. Selection differential and selection gains in the selected genotypes were positive for both glossiness and seedling height and were negative for deadhearts and Eggs.

CONCLUSION

The MTSI selected new sources of resistance may constitute a breeding population for providing a dynamic gene pool of different resistance mechanisms for improving shoot fly resistance in sorghum. © 2023 Society of Chemical Industry.

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.

Sorghum breeding in the genomic era: opportunities and challenges

The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.

Variation in production of cyanogenic glucosides during early plant development: A comparison of wild and domesticated sorghum

Domestication has narrowed the genetic diversity found in crop wild relatives, potentially reducing plasticity to cope with a changing climate. The tissues of domesticated sorghum (Sorghum bicolor), especially in younger plants, are cyanogenic and potentially toxic. Species of wild sorghum produce lower levels of the cyanogenic glucoside (CNglc) dhurrin than S. bicolor at maturity, but it is not known if this is also the case during germination and early growth. CNglcs play multiple roles in primary and specialised metabolism in domesticated sorghum and other crop plants. In this study, the temporal and spatial distribution of dhurrin in wild and domesticated sorghum at different growth stages was monitored in leaf, sheath and root tissues up to 35 days post germination using S. bicolor and the wild species S. brachypodum and S. macrospermum as the experimental systems. Growth parameters were also measured and allocation of plant total nitrogen (N%) to both dhurrin and nitrate (NO₃^-) was calculated. Negligible amounts of dhurrin were produced in the leaves of the two wild species compared to S. bicolor. The morphology of the two wild sorghums also differed from S. bicolor, with the greatest differences observed for the more distantly related S. brachypodum. S. bicolor had the highest leaf N% whilst the wild species had significantly higher root N%. Allocation of nitrogen to dhurrin in aboveground tissue was significantly higher in S. bicolor compared to the wild species but did not differ in the roots across the three species. The differences in plant morphology, dhurrin content and re-mobilisation, and nitrate/nitrogen allocation suggest that domestication has affected the functional roles of dhurrin in sorghum.

Molecular, chemical, and physiological analyses of sorghum leaf wax under post-flowering drought stress

Wax accumulation on the sorghum surface plays an important role in drought tolerance by preventing non-stomatal water loss. Thereby, the effect of post-flowering drought stress (PFDS) on the epicuticular wax (EW) amount, relative water content (RWC), chlorophyll, and grain yield in sorghum drought contrasting genotypes were investigated. The experiment was conducted as a split-plot based on randomized complete block design (RCBD) with two water treatments (normal watering and water holding after 50% flowering stage), and three genotypes (Kimia and KGS23 as drought-tolerant and Sepideh as drought-susceptible). Scanning electron microscopy and GC-MS analyses were used to determine the wax crystals density and its compositions, respectively. In addition, based on literature reviews and publicly available datasets, six wax biosynthesis drought stress-responsive genes were chosen for expression analysis. The results showed that the amounts of EW and wax crystals density were increased in Kimia and Sepideh genotypes and no changed in KGS23 genotype under drought stress. Chemical compositions of wax were classified into six major groups including alkanes, fatty acids, aldehydes, esters, alcohols, and cyclic compounds. Alkanes increment in drought-tolerant genotypes led to make an effective barrier against the drought stress to control water losses. In addition, the drought-tolerant genotypes had higher levels of RWC compared to the drought-susceptible ones, resulted in higher yield produced under drought condition. According to the results, SbWINL1, FATB, and CER1 genes play important roles in drought-induced wax biosynthesis. The results of the present study revealed a comprehensive view of the wax and its compositions and some involved genes in sorghum under drought stress.

QTL Mapping of Traits Associated with Dual Resistance to the African Stem Borer (Busseola fusca) and Spotted Stem Borer (Chilo partellus) in Sorghum (Sorghum bicolor)

Sorghum (Sorghum bicolor (L.) Moench) is an important food crop in semi-arid tropics. The crop grain yield ranges from 0.5 t/ha to 0.8 t/ha compared to potential yields of 10 t/ha. The African stem borer Busseola fusca Fuller (Noctuidae) and the spotted stem borer Chilo partellus Swinhoe (Crambidae), are among the most economically important insect pests of sorghum. The two borers can cause 15% - 80% grain yield loss in sorghum. Mapping of QTLs associated with resistance traits to the two stem borers is important towards marker-assisted breeding. The objective of this study was to map QTLs associated with resistance traits to B. fusca and C. partellus in sorghum. 243 F9:10 sorghum RILs derived from ICSV 745 (S) and PB 15520-1 (R) were selected for the study with 4,955 SNP markers. The RILs were evaluated in three sites. Data was collected on leaf feeding, deadheart, exit holes, stem tunnels, leaf toughness, seedling vigour, bloom waxiness, and leaf glossiness. ANOVA for all the traits was done using Genstat statistical software. Insect damage traits and morphological traits were correlated using Pearson's correlation coefficients. Genetic mapping was done using JoinMap 4 software, while QTL analysis was done using PLABQTL software. A likelihood odds ratio (LOD) score of 3.0 was used to declare linkage. Joint analyses across borer species and sites revealed 4 QTLs controlling deadheart formation; 6 controlling leaf feeding damage; 5 controlling exit holes and stem tunneling damages; 2 controlling bloom waxiness, leaf glossiness, and seedling vigour; 4 conditioning trichome density; and 6 conditioning leaf toughness. Joint analyses for B. fusca and C. partellus further revealed that marker CS132-2 colocalised for leaf toughness and stem tunneling traits on QTLs 1 and 2, respectively; thus, the two traits can be improved using the same linked marker. This study recommended further studies to identify gene(s) underlying the mapped QTLs.

Identification of genomic regions associated with shoot fly resistance in maize and their syntenic relationships in the sorghum genome

Shoot fly (Atherigona naqvii) is one of the major insects affecting spring maize in North India and can cause yield loss up to 60 per cent. The genetics of insect resistance is complex as influenced by genotypic background, insect population and climatic conditions. Therefore, quantitative trait loci (QTL) mapping is a highly effective approach for studying genetically complex forms of insect resistance. The objective of the present study was to dissect the genetic basis of resistance and identification of genomic regions associated with shoot fly resistance. A total of 107 F₂ population derived from the cross CM143 (resistant) x CM144 (susceptible) was genotyped with 120 SSR markers. Phenotypic data were recorded on replicated F_2:3 progenies for various component traits imparting resistance to shoot fly at different time intervals. Resistance to shoot fly was observed to be under polygenic control as evidenced by the identification of 19 putative QTLs governed by overdominance to partial dominance and additive gene actions. The major QTLs conditioning shoot fly resistance viz., qDH9.1 (deadheart) and qEC9.1 (oviposition) explaining 15.03 and 18.89 per cent phenotypic variance, respectively were colocalized on chromosome 9. These QTLs are syntenic to regions of chromosome 10 of sorghum which were also accounted for deadheart and oviposition suggesting that the same gene block may be responsible for shoot fly resistance. The candidate genes such as cysteine protease, subtilisin-chymotrypsin inhibitor, cytochrome P450 involved in synthesis of alleochemicals, receptor kinases, glossy15 and ubiquitin-proteasome degradation pathway were identified within the predicted QTL regions. This is the first reported mapping of QTLs conferring resistance to shoot fly in maize, and the markers identified here will be a valuable resource for developing elite maize cultivars with resistance to shoot fly.

Mapping QTLs and Identification of Genes Associated with Drought Resistance in Sorghum

Water limits global agricultural production. Increases in global aridity, a growing human population, and the depletion of aquifers will only increase the scarcity of water for agriculture. Water is essential for plant growth and in areas that are prone to drought, the use of drought-resistant crops is a long-term solution for growing more food for more people with less water. Sorghum is well adapted to hot and dry environments and has been used as a dietary staple for millions of people. Increasing the drought resistance in sorghum hybrids with no impact on yield is a continual objective for sorghum breeders. In this review, we describe the loci, quantitative trait loci (QTLs), or genes that have been identified for traits involved in drought avoidance (water-use efficiency, cuticular wax synthesis, trichome development and morphology, root system architecture) and drought tolerance (compatible solutes, pre- and post-flowering drought tolerance). Many of these identified genes and QTL regions have not been tested in hybrids and the effect of these genes, or their interactions, on yield must be understood in normal and drought-stressed conditions to understand the strength and weaknesses of their utility.

Introgression of Shoot Fly (Atherigona soccata L. Moench) Resistance QTLs into Elite Post-rainy Season Sorghum Varieties Using Marker Assisted Backcrossing (MABC)

Shoot fly (Atherigona soccata L. Moench) is a serious pest in sorghum production. Management of shoot fly using insecticides is expensive and environmentally un-safe. Developing host-plant resistance is the best method to manage shoot fly infestation. Number of component traits contribute for imparting shoot fly resistance in sorghum and molecular markers have been reported which were closely linked to QTLs controlling these component traits. In this study, three QTLs associated with shoot fly resistance were introgressed into elite cultivars Parbhani Moti (= SPV1411) and ICSB29004 using marker assisted backcrossing (MABC). Crosses were made between recurrent parents and the QTL donors viz., J2658, J2614, and J2714. The F₁s after confirmation for QTL presence were backcrossed to recurrent parents and the resultant lines after two backcrosses were selfed thrice for advancement. The foreground selection was carried out in F₁ and BC_nF₁ generations with 22 polymorphic markers. Forty-three evenly distributed simple sequence repeat markers in the sorghum genome were used in background selection to identify plants with higher recurrent parent genome recovery. By using two backcrosses and four rounds of selfing, six BC₂F₄ progenies were selected for ICSB29004 × J2658, five BC₂F₄ progenies were selected for ICSB29004 × J2714 and six BC₂F₄ progenies were selected for Parbhani Moti × J2614 crosses. Phenotyping of these lines led to the identification of two resistant lines for each QTL region present on chromosome SBI-01, SBI-07 and SBI-10 in ICSB 29004 and Parbhani Moti. All the introgression lines (ILs) showed better shoot fly resistance than the recurrent parents and their agronomic performance was the same or better than the recurrent parents. Further, the ILs had medium plant height, desirable maturity with high yield potential which makes them better candidates for commercialization. In the present study, MABC has successfully improved the shoot fly resistance in sorghum without a yield penalty. This is the first report on the use of MABC for improving shoot fly resistance in post-rainy season sorghum.

Host plant quantitative trait loci affect specific behavioral sequences in oviposition by a stem-mining insect

Genetic diversity in quantitative loci associated with plant traits used by insects as cues for host selection can influence oviposition behavior and maternal choice. Host plant selection for oviposition is an important determinant of progeny performance and survival for phytophagous insects. Specific cues from the plant influence insect oviposition behavior; but, to date, no set of host plant quantitative trait loci (QTLs) have been shown to have an effect on behavioral sequences leading to oviposition. Three QTLs in wheat (Triticum aestivum L.) have been identified as influencing resistance to the wheat stem sawfly (WSS) (Cephus cinctus Norton). Wheat near-isogenic lines (NILs) for each of the three QTLs were used to test whether foraging WSS were able to discriminate variation in plant cues resulting from allelic changes. A QTL on chromosome 3B (Qss-msub-3BL) previously associated with stem solidness and larval antibiosis was shown to affect WSS oviposition behavior, host preference, and field infestation. Decreased preference for oviposition was also related to a QTL allele on chromosome 2D (Qwss.msub-2D). A QTL on chromosome 4A (Qwss.msub-4A.1) affected host plant attractiveness to foraging females, but did not change oviposition preference after females landed on the stem. These findings show that oviposition decisions regarding potential plant hosts require WSS females to discriminate signals from the plant associated with allelic variation at host plant quantitative loci. Allele types in a host plant QTL associated with differential survival of immature progeny can affect maternal choices for oviposition. The multidisciplinary approach used here may lead to the identification of plant genes with important community consequences, and may complement the use of antibiosis due to solid stems to control the wheat stem sawfly in agroecosystems.

Host plant quantitative trait loci affect specific behavioral sequences in oviposition by a stem-mining insect

KEY MESSAGE

Genetic diversity in quantitative loci associated with plant traits used by insects as cues for host selection can influence oviposition behavior and maternal choice. Host plant selection for oviposition is an important determinant of progeny performance and survival for phytophagous insects. Specific cues from the plant influence insect oviposition behavior; but, to date, no set of host plant quantitative trait loci (QTLs) have been shown to have an effect on behavioral sequences leading to oviposition. Three QTLs in wheat (Triticum aestivum L.) have been identified as influencing resistance to the wheat stem sawfly (WSS) (Cephus cinctus Norton). Wheat near-isogenic lines (NILs) for each of the three QTLs were used to test whether foraging WSS were able to discriminate variation in plant cues resulting from allelic changes. A QTL on chromosome 3B (Qss-msub-3BL) previously associated with stem solidness and larval antibiosis was shown to affect WSS oviposition behavior, host preference, and field infestation. Decreased preference for oviposition was also related to a QTL allele on chromosome 2D (Qwss.msub-2D). A QTL on chromosome 4A (Qwss.msub-4A.1) affected host plant attractiveness to foraging females, but did not change oviposition preference after females landed on the stem. These findings show that oviposition decisions regarding potential plant hosts require WSS females to discriminate signals from the plant associated with allelic variation at host plant quantitative loci. Allele types in a host plant QTL associated with differential survival of immature progeny can affect maternal choices for oviposition. The multidisciplinary approach used here may lead to the identification of plant genes with important community consequences, and may complement the use of antibiosis due to solid stems to control the wheat stem sawfly in agroecosystems.

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.

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.

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.

Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production

BACKGROUND

Sorghum is a tropical C4 cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism and photoperiod-insensitivity. Quantitative trait loci for these traits have been introgressed from a dwarf temperate donor into hundreds of diverse sorghum landraces to yield the Sorghum Conversion lines. Here, we report the first comprehensive genomic analysis of the molecular changes underlying this adaptation.

RESULTS

We apply genotyping-by-sequencing to 1,160 Sorghum Conversion lines and their exotic progenitors, and map donor introgressions in each Sorghum Conversion line. Many Sorghum Conversion lines carry unexpected haplotypes not found in either presumed parent. Genome-wide mapping of introgression frequencies reveals three genomic regions necessary for temperate adaptation across all Sorghum Conversion lines, containing the Dw1, Dw2, and Dw3 loci on chromosomes 9, 6, and 7 respectively. Association mapping of plant height and flowering time in Sorghum Conversion lines detects significant associations in the Dw1 but not the Dw2 or Dw3 regions. Subpopulation-specific introgression mapping suggests that chromosome 6 contains at least four loci required for temperate adaptation in different sorghum genetic backgrounds. The Dw1 region fractionates into separate quantitative trait loci for plant height and flowering time.

CONCLUSIONS

Generating Sorghum Conversion lines has been accompanied by substantial unintended gene flow. Sorghum adaptation to temperate-zone grain production involves a small number of genomic regions, each containing multiple linked loci for plant height and flowering time. Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel.

Rank regression for analyzing ordinal qualitative data for treatment comparison

ABSTRACT Ordinal qualitative data are often collected for phenotypical measurements in plant pathology and other biological sciences. Statistical methods, such as t tests or analysis of variance, are usually used to analyze ordinal data when comparing two groups or multiple groups. However, the underlying assumptions such as normality and homogeneous variances are often violated for qualitative data. To this end, we investigated an alternative methodology, rank regression, for analyzing the ordinal data. The rank-based methods are essentially based on pairwise comparisons and, therefore, can deal with qualitative data naturally. They require neither normality assumption nor data transformation. Apart from robustness against outliers and high efficiency, the rank regression can also incorporate covariate effects in the same way as the ordinary regression. By reanalyzing a data set from a wheat Fusarium crown rot study, we illustrated the use of the rank regression methodology and demonstrated that the rank regression models appear to be more appropriate and sensible for analyzing nonnormal data and data with outliers.

Molecular tagging and validation of microsatellite markers linked to the low germination stimulant gene (lgs) for Striga resistance in sorghum [Sorghum bicolor (L.) Moench]

Striga is a devastating parasitic weed in Africa and parts of Asia. Low Striga germination stimulant activity, a well-known resistance mechanism in sorghum, is controlled by a single recessive gene (lgs). Molecular markers linked to the lgs gene can accelerate development of Striga-resistant cultivars. Using a high density linkage map constructed with 367 markers (DArT and SSRs) and an in vitro assay for germination stimulant activity towards Striga asiatica in 354 recombinant inbred lines derived from SRN39 (low stimulant) × Shanqui Red (high stimulant), we precisely tagged and mapped the lgs gene on SBI-05 between two tightly linked microsatellite markers SB3344 and SB3352 at a distance of 0.5 and 1.5 cM, respectively. The fine-mapped lgs region was delimited to a 5.8 cM interval with the closest three markers SB3344, SB3346 and SB3343 positioned at 0.5, 0.7 and 0.9 cM, respectively. We validated tightly linked markers in a set of 23 diverse sorghum accessions, most of which were known to be Striga resistant, by genotyping and phenotyping for germination stimulant activity towards both S. asiatica and S. hermonthica. The markers co-segregated with Striga germination stimulant activity in 21 of the 23 tested lines. The lgs locus similarly affected germination stimulant activity for both Striga species. The identified markers would be useful in marker-assisted selection for introgressing this trait into susceptible sorghum cultivars. Examination of the sorghum genome sequence and comparative analysis with the rice genome suggests some candidate genes in the fine-mapped region (400 kb) that may affect strigolactone biosynthesis or exudation. This work should form a foundation for map-based cloning of the lgs gene and aid in elucidation of an exact mechanism for resistance based on low Striga germination stimulant activity.

Next-generation sequencing applications for wheat crop improvement

Bread wheat (Triticum aestivum; Poaceae) is a crop plant of great importance. It provides nearly 20% of the world's daily food supply measured by calorie intake, similar to that provided by rice. The yield of wheat has doubled over the last 40 years due to a combination of advanced agronomic practice and improved germplasm through selective breeding. More recently, yield growth has been less dramatic, and a significant improvement in wheat production will be required if demand from the growing human population is to be met. Next-generation sequencing (NGS) technologies are revolutionizing biology and can be applied to address critical issues in plant biology. Technologies can produce draft sequences of genomes with a significant reduction to the cost and timeframe of traditional technologies. In addition, NGS technologies can be used to assess gene structure and expression, and importantly, to identify heritable genome variation underlying important agronomic traits. This review provides an overview of the wheat genome and NGS technologies, details some of the problems in applying NGS technology to wheat, and describes how NGS technologies are starting to impact wheat crop improvement.

Molecular bases of plant resistance to arthropods

Arthropod-resistant crops provide significant ecological and economic benefits to global agriculture. Incompatible interactions involving resistant plants and avirulent pest arthropods are mediated by constitutively produced and arthropod-induced plant proteins and defense allelochemicals synthesized by resistance gene products. Cloning and molecular mapping have identified the Mi-1.2 and Vat arthropod resistance genes as CC-NBS-LRR (coiled coil-nucleotide binding site-leucine rich repeat) subfamily NBS-LRR resistance proteins, as well as several resistance gene analogs. Genetic linkage mapping has identified more than 100 plant resistance gene loci and linked molecular markers used in cultivar development. Rice and sorghum arthropod-resistant cultivars and, to a lesser extent, raspberry and wheat cultivars are components of integrated pest management (IPM) programs in Asia, Australia, Europe, and North America. Nevertheless, arthropod resistance in most food and fiber crops has not been integrated due primarily to the application of synthetic insecticides. Plant and arthropod genomics provide many opportunities to more efficiently develop arthropod-resistant plants, but integration of resistant cultivars into IPM programs will succeed only through interdisciplinary collaboration.

Mapping of shoot fly tolerance loci in sorghum using SSR markers

Sorghum (Sorghum bicolor (L.) Moench) is one of the most important crops in the semiarid regions of the world. One of the important biotic constraints to sorghum production in India is the shoot fly which attacks sorghum at the seedling stage. Identification of the genomic regions containing quantitative trait loci (QTLs) for resistance to shoot fly and the linked markers can facilitate sorghum improvement programmes through marker-assisted selection. A simple sequence repeat (SSR) markerbased skeleton linkage map of two linkage groups of sorghum was constructed in a population of 135 recombinant inbred lines (RIL) derived from a cross between IS18551 (resistant to shoot fly) and 296B (susceptible to shoot fly). A total of 14 SSR markers, seven each on linkage groups A and C were mapped. Using data of different shoot fly resistance component traits, one QTL which is common for glossiness, oviposition and dead hearts was detected following composite interval mapping (CIM) on linkage group A. The phenotypic variation explained by this QTL ranged from 3.8%-6.3%. Besides the QTL detected by CIM, two more QTLs were detected following multi-trait composite interval mapping (MCIM), one each on linkage groups A and C for the combinations of traits which were correlated with each other. Results of the present study are novel as we could find out the QTLs governing more than one trait (pleiotropic QTLs). The identification of pleiotropic QTLs will help in improvement of more than one trait at a time with the help of the same linked markers. For all the QTLs, the resistant parent IS18551 contributed resistant alleles.

Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

Identification and validation of genomic regions that affect shoot fly resistance in sorghum [Sorghum bicolor (L.) Moench]

Shoot fly is one of the most important pests affecting the sorghum production. The identification of quantitative trait loci (QTL) affecting shoot fly resistance enables to understand the underlying genetic mechanisms and genetic basis of complex interactions among the component traits. The aim of the present study was to detect QTL for shoot fly resistance and the associated traits using a population of 210 RILs of the cross 27B (susceptible) × IS2122 (resistant). RIL population was phenotyped in eight environments for shoot fly resistance (deadheart percentage), and in three environments for the component traits, such as glossiness, seedling vigor and trichome density. Linkage map was constructed with 149 marker loci comprising 127 genomic-microsatellite, 21 genic-microsatellite and one morphological marker. QTL analysis was performed by using MQM approach. 25 QTL (five each for leaf glossiness and seedling vigor, 10 for deadhearts, two for adaxial trichome density and three for abaxial trichome density) were detected in individual and across environments. The LOD and R (2) (%) values of QTL ranged from 2.44 to 24.1 and 4.3 to 44.1%, respectively. For most of the QTLs, the resistant parent, IS2122 contributed alleles for resistance; while at two QTL regions, the susceptible parent 27B also contributed for resistance traits. Three genomic regions affected multiple traits, suggesting the phenomenon of pleiotrophy or tight linkage. Stable QTL were identified for the traits across different environments, and genetic backgrounds by comparing the QTL in the study with previously reported QTL in sorghum. For majority of the QTLs, possible candidate genes were identified. The QTLs identified will enable marker assisted breeding for shoot fly resistance in sorghum.

Sorghum insect problems and management

Sorghum (Sorghum bicolor) has high levels of starch, sugar, and fiber and is one of the most important energy crops in the world. Insect damage is one of the challenges that impacts sorghum biomass production. There are at least 150 insect species that can infest sorghum varieties worldwide. These insects can complete several generations within a growing season, they target various parts of sorghum plants at developmental stages, and they cause significant biomass losses. Genetic research has revealed the existence of resistant genetics in sorghum and insect tolerant sorghum varieties have been identified. Various control methods have been developed, yet more effective management is needed for increasing sorghum biomass production. Although there are no transgenic sorghum products on the market yet, biotechnology has been recognized as an important tool for controlling insect pests and increasing sorghum production.

Location of major effect genes in sorghum (Sorghum bicolor (L.) Moench)

Major effect genes are often used for germplasm identification, for diversity analyses and as selection targets in breeding. To date, only a few morphological characters have been mapped as major effect genes across a range of genetic linkage maps based on different types of molecular markers in sorghum (Sorghum bicolor (L.) Moench). This study aims to integrate all available previously mapped major effect genes onto a complete genome map, linked to the whole genome sequence, allowing sorghum breeders and researchers to link this information to QTL studies and to be aware of the consequences of selection for major genes. This provides new opportunities for breeders to take advantage of readily scorable morphological traits and to develop more effective breeding strategies. We also provide examples of the impact of selection for major effect genes on quantitative traits in sorghum. The concepts described in this paper have particular application to breeding programmes in developing countries where molecular markers are expensive or impossible to access.