Genetic Improvement of Pearl Millet for Grain and Forage Production: Cytogenetic Manipulation and Heterosis Breeding

Pearl millet, Pennisetum glaucum (L.) R. Brown (= Pennisetum typhoides (Burm.) Stapf et Hubb.), is the most important member of the genus Pennisetum of the tribe Paniceae in the family Poaceae. The name Pennisetum was derived as a hybrid of two Latin words — penna , meaning feather, and seta , meaning bristle — and describes the typically feathery bristles of its species (Jauhar 1981a). Pearl millet is the sixth most important cereal crop in the world, ranking after wheat, rice, maize, barley, and sorghum. It is a valuable grain and fodder crop and is cultivated in many parts of the world, although in the U.S. it is grown primarily as a forage crop on less than 1 million ha. In tropical and warm-temperature regions of Australia and some other countries, it is also grown as a forage crop (Jauhar 1981a). Pearl millet is an ideal organism for basic and applied research. In their extensive reviews, Jauhar (1981a) and Jauhar and Hanna (1998) compiled the available literature on cytogenetics and breeding of pearl millet and related species. This article covers some basic aspects of cytogenetics of pearl millet, its cytogenetic manipulation with a view to enrich it with alien genes, aspects of heterosis breeding facilitated by the cytoplasmic-nuclear male sterility (CMS) system and possibly by apomixis, and direct gene transfer into otherwise superior cultivars

Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome

<p>Abstract</p> <p>Background</p> <p>Apomixis, asexual seed production in plants, holds great potential for agriculture as a means to fix hybrid vigor. Apospory is a form of apomixis where the embryo develops from an unreduced egg that is derived from a somatic nucellar cell, the aposporous initial, via mitosis. Understanding the molecular mechanism regulating aposporous initial specification will be a critical step toward elucidation of apomixis and also provide insight into developmental regulation and downstream signaling that results in apomixis. To discover candidate transcripts for regulating aposporous initial specification in <it>P. squamulatum</it>, we compared two transcriptomes derived from microdissected ovules at the stage of aposporous initial formation between the apomictic donor parent, <it>P. squamulatum </it>(accession PS26), and an apomictic derived backcross 8 (BC₈) line containing only the Apospory-Specific Genomic Region (ASGR)-carrier chromosome from <it>P. squamulatum</it>. Toward this end, two transcriptomes derived from ovules of an apomictic donor parent and its apomictic backcross derivative at the stage of apospory initiation, were sequenced using 454-FLX technology.</p> <p>Results</p> <p>Using 454-FLX technology, we generated 332,567 reads with an average read length of 147 base pairs (bp) for the PS26 ovule transcriptome library and 363,637 reads with an average read length of 142 bp for the BC₈ovule transcriptome library. A total of 33,977 contigs from the PS26 ovule transcriptome library and 26,576 contigs from the BC₈ovule transcriptome library were assembled using the Multifunctional Inertial Reference Assembly program. Using stringent <it>in silico </it>parameters, 61 transcripts were predicted to map to the ASGR-carrier chromosome, of which 49 transcripts were verified as ASGR-carrier chromosome specific. One of the alien expressed genes could be assigned as tightly linked to the ASGR by screening of apomictic and sexual F₁s. Only one transcript, which did not map to the ASGR, showed expression primarily in reproductive tissue.</p> <p>Conclusions</p> <p>Our results suggest that a strategy of comparative sequencing of transcriptomes between donor parent and backcross lines containing an alien chromosome of interest can be an efficient method of identifying transcripts derived from an alien chromosome in a chromosome addition line.</p

The Peanut Genome Consortium and Peanut Genome Sequence: Creating a better future through global food security

The competitiveness of peanuts has been threatened by losses in productivity and quality. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to global in 2006 to address these issues beginning with marker development and genetic map improvement. Ultimately, the peanut genome sequencing project was launched in 2012 by Peanut Genome Consortium, a coalition of international scientists and stakeholders that guide and implement research in Peanut Genome Project (PGP) as an integral program of International Peanut Genome Initiative (IPGI). IPGI has over 135 members in 20 countries at 79 institutions and is a committed step by the world-wide peanut research community to meet the needs of the peanut industry. PGP goals are: 1) a high quality tetraploid reference genome sequence, 2) high throughput genome and transcriptome characterization of tetraploid and diploid, 3) phenotypic trait association with genetic haplotypes, 4) interactive bioinformatic resources. The outcome will enable molecular breeding for enhancing peanut genetic improvement. The large size (2.8 Gb) and allotetraploid nature of peanut genome are challenges for peanut assembly. Therefore an integrated approach has been deployed that complements whole genome sequencing with BAC x BAC, GWAS with Recombinant Inbred Lines, and emerging sequencing technologies to bring the assembly together. SNP discovery also will contribute to a high-density genetic map for chromosome level assembly

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut ( Arachis hypogaea )

Multiparental genetic mapping populations such as nested-association mapping (NAM) havegreat potential for investigating quantitative traits and associated genomic regions leading torapid discovery of candidate genes and markers. To demonstrate the utility and power of thisapproach, two NAM populations, NAM_Tifrunner and NAM_Florida-07, were used for dissectinggenetic control of 100-pod weight (PW) and 100-seed weight (SW) in peanut. Two high-densitySNP-based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner andNAM_Florida-07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effectQTLs for PW and SW, respectively, in NAM_Florida-07. Most of the QTLs associated with PW andSW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide associationstudy (GWAS) analysis identified 19 and 28 highly significant SNP–trait associations (STAs) inNAM_Tifrunner and 11 and 17 STAs in NAM_Florida-07 for PW and SW, respectively. Thesesignificant STAs were co-localized, suggesting that PW and SW are co-regulated by severalcandidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstratesthe utility of NAM population for genetic dissection of complex traits and performing high-resolution trait mapping in peanut

High-Throughput Canopy and Belowground Phenotyping of a Set of Peanut CSSLs Detects Lines with Increased Pod Weight and Foliar Disease Tolerance

We deployed field-based high-throughput phenotyping (HTP) techniques to acquire trait data for a subset of a peanut chromosome segment substitution line (CSSL) population. Sensors mounted on an unmanned aerial vehicle (UAV) were used to derive various vegetative indices as well as canopy temperatures. A combination of aerial imaging and manual scoring showed that CSSL 100, CSSL 84, CSSL 111, and CSSL 15 had remarkably low tomato spotted wilt virus (TSWV) incidence, a devastating disease in South Georgia, USA. The four lines also performed well under leaf spot pressure. The vegetative indices showed strong correlations of up to 0.94 with visual disease scores, indicating that aerial phenotyping is a reliable way of selecting under disease pressure. Since the yield components of peanut are below the soil surface, we deployed ground penetrating radar (GPR) technology to detect pods non-destructively. Moderate correlations of up to 0.5 between pod weight and data acquired from GPR signals were observed. Both the manually acquired pod data and GPR variables highlighted the three lines, CSSL 84, CSSL 100, and CSSL 111, as the best-performing lines, with pod weights comparable to the cultivated check Tifguard. Through the combined application of manual and HTP techniques, this study reinforces the premise that chromosome segments from peanut wild relatives may be a potential source of valuable agronomic trait

Genome‑wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection

Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several years of breeding for GRD resistance, the genetics of the disease is not fully understood. The objective of the current study was to use the African core collection to establish the level of genetic variation in their response to GRD, and to map genomic regions responsible for the observed resistance. The African groundnut core genotypes were screened across two GRD hotspot locations in Uganda (Nakabango and Serere) for 3 seasons. The Area Under Disease Progress Curve combined with 7523 high quality SNPs were analyzed to establish marker-trait associations (MTAs). Genome-Wide Association Studies based on Enriched Compressed Mixed Linear Model detected 32 MTAs at Nakabango: 21 on chromosome A04, 10 on B04 and 1 on B08. Two of the significant markers were localised on the exons of a putative TIR-NBS-LRR disease resistance gene on chromosome A04. Our results suggest the likely involvement of major genes in the resistance to GRD but will need to be further validated with more comprehensive phenotypic and genotypic datasets. The markers identified in the current study will be developed into routine assays and validated for future genomics-assisted selection for GRD resistance in groundnut

Genomics of Peanut, a Major Source of Oil and Protein

Peanut, as a source of oil and protein, is the second-most important grain legume cultivated. The perceived lack of molecular variation in the cultivated species had, until recently, resulted in a focus on characterization and mapping of wild species and on transformation of peanut with genes for improved disease resistance. With development of simple sequence repeats and potentially single nn- cleotide polymorphism-based markers and improved minicore collections, the focus is shifting towards the molecular characterization of the cultivated species. The de- velopment of large-inset libraries, expressed sequence tags. genomic clone libraries, characterized mutant collections, and hioinlrmatics is e\jiected to ads ance peanut genomics