Evaluating testcross performance and genetic divergence of lines derived from reciprocal tropical maize composites

The development of hybrids with enhanced expression of heterosis depends on the genetic background of the source population and the effectiveness of a breeding scheme used to identify and use divergent inbred lines with good combining ability. The present study was conducted to examine the potential of improved tropical reciprocal composites as sources of inbred lines for developing productive hybrids. Thirty-six S4 lines derived from the third RRS cycle of each composite were crossed in pairs to form 36 testcrosses, which were evaluated along with commonly grown commercial hybrids in Nigeria across nine test environments. Results showed consistent ranking of testcrosses for grain yield and other traits across the diverse test environments. The best 22 testcrosses produced 21% to 51% more grain yields than the highest yielding commercial hybrid. Several testcrosses combined high grain yields with other desirable agronomic traits. The SSR and SNP markers used in the present study detected a broad range of genetic diversity among the 72 S4 lines, which was structured along the two composites. The two markers portrayed similar trends in determining genetic distance estimates and detecting composite-specific alleles in the S4 lines. These results highlight the potential of improved reciprocal composites as sources of new and divergent parents for developing productive hybrids and as sources of novel alleles for broadening and diversifying the genetic base of adapted germplasm to sustain genetic gain in productivity of hybrids in WCA

Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

Background Selection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic changes, and the potential for future improvement, using experimental populations that attempt to undo selection through the randomizing effects of recombination. Results We bred the NIAB Diverse MAGIC multi-parent population comprising over 500 recombinant inbred lines, descended from sixteen historical UK bread wheat varieties released between 1935 and 2004. We sequence the founders’ genes and promoters by capture, and the MAGIC population by low-coverage whole-genome sequencing. We impute 1.1 M high-quality SNPs that are over 99% concordant with array genotypes. Imputation accuracy only marginally improves when including the founders’ genomes as a haplotype reference panel. Despite capturing 73% of global wheat genetic polymorphism, 83% of genes cluster into no more than three haplotypes. We phenotype 47 agronomic traits over 2 years and map 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Around half of these overlap known quantitative trait loci. Most traits exhibit extensive polygenicity, as revealed by multi-locus shrinkage modelling. Conclusions Our results are consistent with a gene pool of low haplotypic diversity, containing few novel loci of large effect. Most past, and projected future, phenotypic changes arising from existing variation involve fine-scale shuffling of a few haplotypes to recombine dozens of polygenic alleles of small effect. Moreover, extensive pleiotropy means selection on one trait will have unintended consequences, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break unfavorable trait-trait associations

Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea

Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi-parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013–14 and 2014–15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high-density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome-wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity-by-descent (IBD)-based mixed model approach was used to map quantitative trait loci (QTLs). The IBD-based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker-trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas

Management of Giant Cell Tumour: A Nigerian Experience

Giant cell tumours (GCT) are the commonest bone tumours worldwide. It is rarely malignant but when it does it progresses to fibrosarcoma with high mortality. Otherwise it causes poor cosmesis, disability and pathological fractures. A total of 19 cases of histologically established Giant cell tumour of the bone were reviewed prospectively in a 5 year study. 14 cases were benign, 4 malignant and one was a malignant transformation. Lesions around the knee accounted for 42.2% of the cases, but the radius was the commonest single bone affected with 26.3%. Eleven patients had curettage, five of them had autogenous bone grafting while the remaining six had bone grafting and plate augmentation. One patient had fore-quarter amputation while seven had tumour resection. There was no recurrence recorded among those that had currretage and autogenous bone grafting. 33% of those that had curettage and bone cementing as well as 16.6% of those that had resection presented with recurrence. One patient died within 3 months of surgery due to metastasis to the lungs, liver and spleen. Mean follow up was 9.2 months (range of 2 to 60 months). With early presentation, curretage and bone grafting is often effective; late presentation however has an increased risk of recurrence due to soft tissue involvement, dearth of investigative tools and financial constraints. Nigerian Journal of Surgical Sciences Vol. 17 (2) 2007: pp. 91-9

Challenges in the diagnosis and management of musculoskeletal tumours in Nigeria

The management of musculoskeletal tumours is important because of the high mortality rates associated with the available treatment modalities. A 5-year prospective study of bone and soft-tissue tumours is presented, along with the difficulties encountered in diagnosis and treatment. There were 71 patients (male:female ratio of 1.7:1, age range 5–85 years, mean age 32 years) with an average duration of 24.7 weeks (range 1 day to 34 years) before presentation. No patient had computed tomography (CT) scanning or magnetic resonance imaging (MRI) due to financial constraints, 95% had biopsies and X-rays, 15% could afford chemotherapy/ror chemotherapy is a sad consequence. 50% agreed to amputation. In the soft-tissue sarcoma group, only one of three patients could pay for limb-sparing surgery. In the benign group, 65% had limb-sparing surgeries and 15% had amputation. Fifty percent (50%) of patients were lost to follow up within 3 months and 39% of the malignant group died within the same period. Musculoskeletal tumours are a reality in our environment and a significant portion of our population have financial limitations. Ignorance and cultural beliefs promote late presentation to our hospitals, which are poorly equipped to give optimal care, despite the presence of trained personnel

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding