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

Improvement of little millet (Panicum sumatrense) using novel omics platform and genetic resource integration

MAIN CONCLUSION

This article explores possible future initiatives, such as the development of targeted breeding and integrated omics approach to boost little millet production, nutritional value, and environmental adaptation. Little millet (P. sumatrense) is a staple grain in many parts of Asia and Africa owing to its abundance in vitamins and minerals and its ability to withstand harsh agro-ecological conditions. Enhancing little millet using natural resources and novel crop improvement strategy is an effective way of boosting nutritional and food security. To understand the genetic makeup of the crop and figure out important characteristics linked to nutritional value, biotic and abiotic resistance, and production, researchers in this field are currently resorting on genomic technology. These realizations have expedited the crop's response to shifting environmental conditions by enabling the production of superior cultivars through targeted breeding. Going forward, further improvements in breeding techniques and genetics may boost the resilience, nutritional content, and production of little millet, which would benefit growers and consumers alike. The research and development on little millet improvement using novel omics platform and the integration of genetic resources are summarized in this review paper. Improved cultivars of little millet that satisfy changing farmer and consumer demands have already been developed through the use of these novel breeding strategies. This article also explores possible future initiatives, such as the development of targeted breeding, genomics, and sustainable agriculture methods. The potential for these measures to boost little millet's overall production, nutritional value, and climate adaptation will be extremely helpful in addressing nutritional security.

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.

Selection Signatures in Chinese Sorghum Reveals Its Unique Liquor-Making Properties

Chinese sorghum (S. bicolor) has been a historically critical ingredient for brewing famous distilled liquors ever since Yuan Dynasty (749 ∼ 652 years BP). Incomplete understanding of the population genetics and domestication history limits its broad applications, especially that the lack of genetics knowledge underlying liquor-brewing properties makes it difficult to establish scientific standards for sorghum breeding. To unravel the domestic history of Chinese sorghum, we re-sequenced 244 Chinese sorghum lines selected from 16 provinces. We found that Chinese sorghums formed three distinct genetic sub-structures, referred as the Northern, the Southern, and the Chishui groups, following an obviously geographic pattern. These sorghum accessions were further characterized in liquor brewing traits and identified selection footprints associated with liquor brewing efficiency. An importantly selective sweep region identified includes several homologous genes involving in grain size, pericarp thickness, and architecture of inflorescence. Our result also demonstrated that pericarp strength rather than grain size determines the ability of the grains to resist repeated cooking during brewing process. New insight into the traits beneficial to the liquor-brewing process provides both a better understanding on Chinese sorghum domestication and a guidance on breeding sorghum as a multiple use crop in China.

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.

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.

Feeding preference of Spodoptera frugiperda on different sorghum genotypes

ABSTRACT The resistance of plants to pests is a feature of great importance for agriculture, as it reduces costs with insecticides and promotes increased yield resulting in higher profits. This work aimed to evaluate the feeding preference of the Spodoptera frugiperda caterpillar by different sorghum genotypes. The experiment was carried out at the Entomology Laboratory of Universidade Estadual de Mato Grosso do Sul, at University Unit of Cassilândia, from March to June 2016. The experimental design was completely randomized with ten replicates. The treatments were composed by seven sorghum genotypes: Agromen 50A40, Agromen 50A50, DOW 1G100, DOW 1G220, DOW 1G233, XB 6022 and LG 6310. Evaluations were performed with 1st instar caterpillars. The number of caterpillars that settled in the genotypes at 5, 10, 15, 20, 25, 30, 60 minutes and 24 hours after the infestation was recorded. The feeding preference index and the fresh leaf mass consumed were estimated. The Agromen 50A40 genotype showed lower attractiveness rating for the S. frugiperda among all evaluated sorghum genotypes.

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.

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.