Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags

<p>Abstract</p> <p>Background</p> <p>Pearl millet [<it>Pennisetum glaucum </it>(L.) R. Br.] is a staple food and fodder crop of marginal agricultural lands of sub-Saharan Africa and the Indian subcontinent. It is also a summer forage crop in the southern USA, Australia and Latin America, and is the preferred mulch in Brazilian no-till soybean production systems. Use of molecular marker technology for pearl millet genetic improvement has been limited. Progress is hampered by insufficient numbers of PCR-compatible co-dominant markers that can be used readily in applied breeding programmes. Therefore, we sought to develop additional SSR markers for the pearl millet research community.</p> <p>Results</p> <p>A set of new pearl millet SSR markers were developed using available sequence information from 3520 expressed sequence tags (ESTs). After clustering, unigene sequences (2175 singlets and 317 contigs) were searched for the presence of SSRs. We detected 164 sequences containing SSRs (at least 14 bases in length), with a density of one per 1.75 kb of EST sequence. Di-nucleotide repeats were the most abundant followed by tri-nucleotide repeats. Ninety primer pairs were designed and tested for their ability to detect polymorphism across a panel of 11 pairs of pearl millet mapping population parental lines. Clear amplification products were obtained for 58 primer pairs. Of these, 15 were monomorphic across the panel. A subset of 21 polymorphic EST-SSRs and 6 recently developed genomic SSR markers were mapped using existing mapping populations. Linkage map positions of these EST-SSR were compared by homology search with mapped rice genomic sequences on the basis of pearl millet-rice synteny. Most new EST-SSR markers mapped to distal regions of linkage groups, often to previous gaps in these linkage maps. These new EST-SSRs are now are used by ICRISAT in pearl millet diversity assessment and marker-aided breeding programs.</p> <p>Conclusion</p> <p>This study has demonstrated the potential of EST-derived SSR primer pairs in pearl millet. As reported for other crops, EST-derived SSRs provide a cost-saving marker development option in pearl millet. Resources developed in this study have added a sizeable number of useful SSRs to the existing repertoire of circa 100 genomic SSRs that were previously available to pearl millet researchers.</p

Development of new sources of tetraploid Arachis to broaden the genetic base of cultivated groundnut (Arachis hypogaea L.)

Groundnut, an important crop of many countries of the world, is susceptible to a range of diseases and pests. High levels of resistances are not available in the cultivated gene pool as the crop is said to have a narrow genetic base. Narrow genetic base is attributed to the evolution of the crop which took place by the combination of A and B genome species, and later doubling their chromosome number, giving rise to tetraploid cultivated groundnut. Direct utilization of cross-compatible wild relatives, which are diploids, to broaden the genetic base and introduction of useful traits, is not a straight-forward process due to ploidy differences between the cultivated species and wild relatives. Hence amphiploids and autotetraploids were created by not only combining the putative genomes, but many other A and B genome species, thus producing a highly variable population of tetraploid groundnuts also called new sources of Arachis hypogaea. This study describes the development and characterization of newly generated tetraploid groundnuts and the level of molecular diversity as assessed by DArT marker

QTL and QTL × Environment Effects on Agronomic and Nitrogen Acquisition Traits in Rice

Agricultural environments deteriorate due to excess nitrogen application. Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input. Rice genotypes respond variably to soil available nitrogen. The present study attempted quantification of genotype × nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits. Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena. Three nitrogen regimes namely, native (0 kg/ha; no nitrogen applied), optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments. The parents and DH lines were significantly varying for all traits under different nitrogen regimes. All traits except plant height recorded significant genotype×environment interaction. Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake. Sixteen QTLs were detected by composite interval mapping. Eleven QTLs showed significant QTL×environment interactions. On chromosome 3, seven QTLs were detected associated with nitrogen use, plant yield and associated traits. A QTL region between markers RZ678, RZ574 and RZ284 was associated with nitrogen use and yield. This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes

Construction of genetic linkage map and QTL analysis of sinksize traits in pearl millet (Pennisetum glaucum)

A linkage map, primarily based on SSCP-SNP markers, was constructed using 188 F2:3 (F2-derived F3) mapping population progenies derived from a cross between two pearl millet inbred lines having diverse pedigrees. The parents had large differences for two sink size traits (grain size and panicle diameter), and also differed for panicle length. The skeleton linkage map covered 1019 cM and it comprised of 44 loci (detected with 24 SSCP-SNP, 10 genomic SSR, 6 EST-SSR and 4 STS primer pairs) distributed across the seven linkage groups. Average adjacent-marker intervals ranged from 14 cM on LG1 to 38 cM on LG6, with an overall mean of 23 cM. Using the F2 linkage map and phenotypic data collected from the F2 and F2:3 generations of the mapping population, a total of 18 putative QTLs were detected for the three sink-size components. Eight QTLs explained 42.7% of observed phenotypic variation for panicle length, with individual QTLs explaining 6.1 to 18.2% using the F2:3 data set. For panicle diameter, 5 QTLs explained 45.8% of observed phenotypic variation with individual QTLs accounting for 6.3 to 30.2%. Similarly for grain size, 5 QTLs explained 29.6% of phenotypic variation with individual QTLs accounting for 6.1 to 8.9%. Genomic regions associated with panicle length, panicle diameter and grain size co-mapped on LG6 between Xpsms88 and Xpsms2270, indicating the existence of a gene or gene cluster with major effects involved in the control of significant proportions of the phenotypic variation for all three sink-size traits. The QTLs for panicle length on LG2 and LG6 (LOD>3 in both F2 and F2:3 data sets), for panicle diameter on LG2 and LG3 (LOD>14 in the F2:3 data set) and for grain size on LG3 and LG6 (LOD>3 in both F2 and F2:3 data sets) were identified as promising candidates for validation prior to possible application in marker-assisted breeding

Does the Vulnerable sun bear Helarctos malayanus damage crops and threaten people in oil palm plantations?

Largely as a result of the expansion of oil palm Elaeis guineensis, forest fragmentation has occurred on a large scale in Borneo. There is much concern about how forest-dependent species, such as the Vulnerable sun bear Helarctos malayanus, can persist in this landscape. The absence of sufficient natural food in forest fragments could drive sun bears into oil palm plantations, where they risk coming into conflict with people. We interviewed oil palm plantation workers and farmers in the Lower Kinabatangan region of Sabah, Malaysian Borneo, to ascertain if sun bears were utilizing plantations, if they were causing damage to the crop, and how the bears were perceived by people. To obtain a comparative baseline we extended these questions to include other species as well. We found that bears were rarely encountered in plantations and were not considered to be destructive to the oil palm crop, although they were generally feared. Other species, such as macaques Macaca spp., bearded pigs Sus barbatus, and elephants Elephas maximus, had more destructive feeding habits. Sun bears could use this readily available food resource without being targeted for retribution, although incidental human-related mortality remains a risk. Although bears could gain some nutritional benefit from oil palm, plantations do not provide the diversity of food and cover available in a natural forest

Third-party vocal intervention in the proboscis monkey (Nasalis larvatus)

Vocal intervention is a triadic social interaction, where a third party responds vocally to a conflict between group members, minimizing the costs of aggression in response to the intervention. Because there is little information on vocal third-party intervention in nonhuman mammals, we investigated whether adult male proboscis monkeys use the bray vocalization as a vocal third-party intervention signal to intervene in intragroup conflicts. First, we audio-recorded 1,811 vocalizations from 17 free-ranging proboscis monkey groups in the Lower Kinabatangan Wildlife Sanctuary, analyzing 378 vocal responses of the adult male to agonistic vocal exchanges (shrieks) of group members. Second, we video- and audio-recorded five habituated groups in the Labuk Bay Proboscis Monkey Sanctuary investigating the context of these vocalizations and the conflict dyads evoking vocal support. We found that adult males of one-male/multifemale groups mainly uttered bray vocalizations, whereas females, immatures, and infants uttered shrieks in intragroup conflicts or in response to other animal species. The adult male uttered significantly more often brays after agonistic shrieks than expected based on the overall occurrence of brays. Brays ended 65% of agonistic conflicts, which were accompanied by vocalizations of the conflict partners and occurred more often after conflicts between females than between offspring. This suggests that the bray functions as a vocal third-party intervention signal for intragroup conflict resolution. We suggest that living in the high canopies of the tropical rainforest might restrict direct access to conflict partners and prevent physical intervention, favoring the evolution of the bray as a third-party vocal intervention signal

Mapping Quantitative Trait Loci Controlling High Iron and Zinc Content in Self and Open Pollinated Grains of Pearl Millet [Pennisetum glaucum (L.) R. Br.]

Pearl millet is a multipurpose grain/fodder crop of the semi-arid tropics, feeding many of the world’s poorest and most undernourished people. Genetic variation among adapted pearl millet inbreds and hybrids suggests it will be possible to improve grain micronutrient concentrations by selective breeding. Using 305 loci, a linkage map was constructed to map QTLs for grain [Fe] and [Zn] using replicated samples of 106 pearl millet RILs (F6) derived from ICMB 841-P3 × 863B-P2. The grains of the RIL population were evaluated for Fe and Zn concentration using atomic absorption spectrophotometer. Grain mineral concentrations ranged from 28.4-124.0 ppm for Fe and 28.7-119.8 ppm for Zn. Similarly,grain Fe and Zn in open pollinated seeds ranged between 22.4-77.4 and 21.9-73.7 ppm, respectively. Mapping with 305 (96 SSRs; 208 DArT) markers detected seven linkage groups covering 1749 cM (Haldane) with an average intermarker distance of 5.73 cM. On the basis of two environment phenotypic data, two co-localized QTLs for Fe and Zn density on LG 3 were identified by composite interval mapping (CIM). Fe QTL explained 19% phenotypic variation, whereas the Zn QTL explained 36% phenotypic variation. Likewise for open pollinated seeds, the QTL analysis led to identification of two QTLs for grain Fe density on LG 3 and 5, and two QTLs for grain Zn density on LG 3 and 7. The total phenotypic variance for Fe and Zn QTLs in open pollinated seeds was 16% and 42%, respectively. Analysis of QTL × QTL and QTL × QTL× environment interactions indicated no major epistasis

Virulence Diversity in North Indian Isolates of Sclerospora Graminicola, the pearl millet Downy Mildew Pathogen

On-farm surveys were conducted in the Uttar Pradesh (India) during the two rainy seasons 2007 and 2008 to monitor pearl millet (Pennisetum glaucum) downy mildew incidence. Twenty-one isolates of Sclerospora graminicola, the pearl millet downy mildew pathogen, were collected from different hybrid cultivars. These isolates were established on seedlings of the highly susceptible line 7042S grown in the greenhouse and were characterized for their virulence diversity using a set of seven host differential lines. Quantitative differences in virulence among pathogen isolates were determined by calculating virulence index (percent disease incidence × latent period-1). Results were submitted to cluster analysis using the Average Linkage method to determine similarity among pathogen isolates. The two highly virulent isolates, Sg 492 from Aligarh and Sg 510 from Badaun, representing geographically diverse locations were selected for use in greenhouse screening of pearl millet breeding lines