Genetic divergence and molecular characterization of sorghum hybrids and their parents for reaction to Atherigona soccata (Rondani).

Simple sequence repeat (SSR) markers linked to quantitative trait loci (QTL) associated with resistance to sorghum shoot fly, Atherigona soccata resistance were used to characterize the genetic and phenotypic diversity of 12 cytoplasmic male-sterile (CMS) and maintainers, 12 restorer lines, and 144 F1 hybrids. The genetic diversity was quite high among the shoot fly-susceptible parents and the hybrids based on them, as indicated by high polymorphic information content (PIC) values, while limited genetic diversity was observed among shoot fly-resistant lines. The phenotypic and genotypic dissimilarity analysis indicated that the shoot fly-resistant and -susceptible parents were 73.2 and 38.5% distinct from each other, and the morphological and genetic distances of certain resistant and susceptible cross combinations was more than their resistant or susceptible parents. Genetic variability among the groups was low (10.8%), but high within groups (89.2%). The genetic and morphological distances suggested that the F1 hybrids were closer to CMS (5 to 12% dissimilar) than the restorer (11 to 87% dissimilar), suggesting that CMS influences the expression of resistance to sorghum shoot fly. The SSR markers can be used to characterize the homologous traits in sorghum germplasm

The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers

The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineënse accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discusse

Opportunities for marker-assisted selection (MAS) to improve the feed quality of crop residues in pearl millet and sorghum

Cereal crop residues (straw, chaff, etc.) are important components of maintenance rations for ruminant livestock in many parts of the world. They are especially important in small-holder crop-livestock production systems in the sub-humid, semi-arid, and arid tropics and subtropics where most of the world's poorest livestock producers and consumers are found. Taking as examples tropically adapted cereals in the crop improvement mandate of the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), namely pearl millet [Pennisetum glaucum (L.) R. Br.] and sorghum [Sorghum bicolor (L.) Moench], this paper explores opportunities for using marker-assisted crop breeding methods to improve the quality and quantity of cereal crop residues for use as ruminant livestock feedstuffs. In the case of pearl millet, ICRISAT has been heavily involved with several UK-based collaborating research institutes, in development and initial application of the molecular genetic tools for marker-assisted breeding. We have obtained some useful experience in quantitative trait loci (QTL) mapping and marker-assisted selection (MAS) for stover yield, foliar disease resistance, and in vitro estimates of the nutritive value of various stover fractions for ruminants. In sorghum, ICRISAT has focused on initiating a large-scale high-throughput marker-assisted backcrossing program for the stay-green component of terminal drought tolerance - a trait that is likely to be associated not only with more stable grain and stover yield, but which is also expected to contribute to maintenance of ruminant nutritional value of stover produced under drought stress conditions. Conventional and marker-assisted breeding for foliar disease resistance is recommended for dual-purpose cereal improvement, or indeed for improvement of the nutritional value of residues for any crop in which these are used as feedstuffs for ruminant livestock. Practical problems faced and proposed ways of dealing with these are discussed

Marker-assisted introgression improves Striga resistance in an Eritrean Farmer-Preferred Sorghum Variety

The parasitic weed Striga hermonthica hampers the production of sorghum, the most important cereal crop in Eritrea. This weed has a complex mode of infestation that adapts to many hosts and environments, complicating conventional breeding for resistance, which is the only form of crop improvement available to Eritrean breeders, but has failed. This study aimed at improving resistance against this parasite by transferring 5 Striga resistant Quantitative Trait Loci (QTLs) from resistance donor N13 to Striga susceptible Farmer-Preferred Sorghum Variety (FPSV) Hugurtay from Eritrea. The method involved backcrossing using marker-assisted selection (MAS) and evaluation of the best introgressed lines for Striga resistance in artificially infested fields. Foreground selection was performed with up to 11 polymorphic simple sequence repeat (SSR) markers linked to Striga resistance QTLs, while background selection was conducted in the BC3F2 generation with 27 polymorphic unlinked SSR markers to identify the best recovery of the recurrent parent (RP) genetic background. Out of 84 BC3F3 lines, L2P3-B, L1P5-A and L2P5P35 performed best with respect to both grain yield and reduced Striga infestation. These lines were more resistant to Striga than Hugurtay, but less resistant than N13. The three lines yielded twice as much as N13, with Area Under Striga Number Progression Curve (AUSNPC) values on average 18% higher than that of N13 and 38% lower than that of Hugurtay. This suggests that the introgressed QTLs conferred significant Striga resistance and yield advantage to these BC3F3 backcross progenies under Striga pressure. These lines have good potential for future release and demonstrate that when MAS is available to conventional breeders, even in countries with no genotyping facilities, it is a useful tool for enhancement, expediency and precision in crop improvement

Host plant resistance to insects in sorghum: present status and need for future research

Research on the identification of sources of resistance to insect pests of sorghum (i.e.cytoplasmic male sterile lines and wild relatives), and on the improvement and induction of insect pest resistance in sorghum by marker-assisted selection and genetic engineering is summarized. Future prospects are mentioned

Improved hardness results for the guided local Hamiltonian problem

Estimating the ground state energy of a local Hamiltonian is a central problem in quantum chemistry. In order to further investigate its complexity and the potential of quantum algorithms for quantum chemistry, Gharibian and Le Gall (STOC 2022) recently introduced the guided local Hamiltonian problem (GLH), which is a variant of the local Hamiltonian problem where an approximation of a ground state (which is called a guiding state) is given as an additional input. Gharibian and Le Gall showed quantum advantage (more precisely, BQP-completeness) for GLH with 6-local Hamiltonians when the guiding state has fidelity (inverse-polynomially) close to 1/2 with a ground state. In this paper, we optimally improve both the locality and the fidelity parameter: we show that the BQP-completeness persists even with 2-local Hamiltonians, and even when the guiding state has fidelity (inverse-polynomially) close to 1 with a ground state. Moreover, we show that the BQP-completeness also holds for 2-local physically motivated Hamiltonians on a 2D square lattice or a 2D triangular lattice. Beyond the hardness of estimating the ground state energy, we also show BQP-hardness persists when considering estimating energies of excited states of these Hamiltonians instead. Those make further steps towards establishing practical quantum advantage in quantum chemistry

Exploiting rice–sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map

The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag (EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50 homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using parental pairs of two existing sorghum mapping populations. About 28% of these new markers detected polymorphism in this 4-entry panel. A subset of 55 polymorphic EST-derived SSR markers were mapped onto the existing skeleton map of a recombinant inbred population derived from cross N13 × E 36-1, which is segregating for Striga resistance and the stay-green component of terminal drought tolerance. These new EST-derived SSR markers mapped across all 10 sorghum linkage groups, mostly to regions expected based on prior knowledge of rice–sorghum synteny. The ESTs from which these markers were derived were then mapped in silico onto the aligned sorghum genome sequence, and 88% of the best hits corresponded to linkage-based positions. This study demonstrates the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related crop species for which sufficient genomic tools are not availabl

Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies