Genotype identification and assessment of genetic relationships in pearl millet [Pennisetum glaucum (L.) R. Br] using microsatellites and RAPDs

 The potential of DNA markers such as microsatellites, minisatellites and RAPDs was investigated in pearl millet [Pennisetum glaucum (L.) R. Br] with respect to their abundance and variability. Southern analysis, using 22 different di-, tri-, tetra- and penta-oligonucleotide probes and five minisatellite probes, identified (GATA)₄ as the most useful probe for the detection of multiple polymorphic fragments among pearl millet cultivars and landraces from India. The clustering patterns of pearl millet cultivars and landraces based on (GATA)₄ and RAPD (randomly amplified polymorphic DNA) markers differed. The landraces, representing eight states in India, could not be grouped based on their geographical distribution with the DNA markers. RAPD analysis revealed a high degree of genetic diversity among the cultivars and landraces employed in this study. The probability of an identical match by chance for any two genotypes using (GATA)₄ and RAPDs was 3.02×10^-20 for cultivars and 5.2×10^-9 for landraces. The microsatellite (GATA)₄ and RAPDs provide useful tools for genotype identification and for the assessment of genetic relationships in pearl millet. Received: 19 October 1997 / Accepted: 9 December 1997     

Effect of the timing of water deficit on growth, phenology and yield of pearl millet (Pennisetum glaucum (L.) R. Br.) grown in Sahelian conditions

Several studies conducted under high input conditions have indicatedlittle susceptibility of pearl millet to water deficit untillearly grain filling, because the losses in main shoot productionwere fully compensated by increased tiller fertility. The presentstudy assessed the impact of water deficits at three developmentstages: prior to flowering (S30), at the beginning of flowering(S45), and at the end of flowering (S60) in pearl millet grownin experimental conditions similar to Sahelian farming conditions.It included a control irrigation treatment simulating the naturaldistribution of rainfall throughout the cropping season. Bothbiomass production and grain yield were severely reduced byS30 and S45, while S60 had no effect. In S30 and S45, the floweringof tillers was delayed or totally inhibited. In both of thesetreatments, the low number of productive tillers did not compensatefor damage to panicle initiation and flowering of the main shoot.All treatments maintained green leaves on the main shoot duringthe grain filling period, and in S30 leaf growth recovered frommid-season drought. These results illustrate how pearl milletmostly escapes drought by matching its phenology to the meanrainfall distribution in the Sahel. In the case of mid-seasondrought, some late productive tillers and the maintenance ofgreen leaf biomass of the main shoots limited, but did not overcome,the yield losses. This study stresses the importance of agro-ecologicalconditions in control treatments, particularly the water regimeand crop density, when assessing crop drought resistance. Key words: Drought resistance strategy, experimental conditions, main shoots, tillers, Pennisetum glaucum     

Assessment of cytoplasmic differences of near-isonuclear male-sterile lines in pearl millet

Four near-isonuclear polycytoplasmic versions of 81A and two of Pb 402A male-sterile lines of pearl millet (Pennisetum typhoides) were used in factorial matings with five inbred male testers in different combinations in three sets. The cytoplasmic differences were studied for several agronomic traits using mean values and general combining effects (gca) of male-sterile lines, and specific combining ability effects of hybrids. The fertility/ sterility behaviour of different male-sterile lines in crosses with common male parents was also studied. Significant differences among near-isonuclear polycytoplasmic lines were observed in mean values for a few traits such as plant height, leaf length and peduncle length, but the differences for combining ability were more pronounced. The A₃ cytoplasm was a better general combiner than the A₂ cytoplasm for grain yield and both A₂ and A₃ cytoplasms were better general combiners for leaf length and peduncle length. In addition, superiority of A₃ cytoplasm for gca was observed for plant height and ear characters over the A₂ cytoplasm in set II. A differential behaviour of cytoplasms, both in combination with a common pollinator and across pollinators, was observed for several traits. The results provide evidence for the distinctiveness of different cytoplasmic sources in pearl millet and for the influence of cytoplasmic factors on the phenotypic expression of nuclear genes. A diversification of male sterility sources in the breeding of pearl millet hybrids is suggested.     

Inference of domestication history and differentiation between early‐ and late‐flowering varieties in pearl millet

Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early‐ and late‐flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early‐ and late‐flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation‐by‐distance pattern. Conversely, our data brought evidence for two well‐differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.     

Flowering Phenology and Gender Variation in Pennisetum typhoides

Because of the modular structure of pearl millet (an annual grass crop, Poaceae), different tillers of a plant share the same genotype but are subjected to different environmental conditions during their maturation. This allows investigation of the effects of tiller flowering phenology on allocation to resource-producing photosynthetic biomass, sexual functions, and thus tiller gender. All tillers of plants of two families collected from individual maternal plants (represented by 33 and 31 plants each) were analyzed. In both families, allocation to aboveground vegetative biomass decreased as flowering was delayed. On average, late-flowering tillers were 65% smaller than the first ones to flower. The proportion of biomass allocated to reproduction significantly increased with the flowering rank of the tillers, suggesting that translocations of assimilates occurred between early- and late-flowering tillers. In both families, late-flowering tillers produced significantly fewer pollen grains per stamen than early-flowering ones, and female reproductive allocation (expressed as seed mass per tiller) was also affected by flowering phenology. Tillers became increasingly female as flowering phenology progressed. This gender variation is possibly adaptive because pollination efficiency is maximized by plant height. Natural selection may favor a shift toward femaleness to maximize reproductive fitness in small, late-developing tillers.     

Genetic diversity and its relationship to hybrid performance and heterosis in rice as revealed by PCR-based markers

Ten elite inbred lines (four japonica, six indica), chosen from those widely used in the hybrid rice breeding program at Human Hybrid Rice Research Center in China, were crossed to produce all possible hybrids excluding reciprocals. The 45 F₁ hybrids along with the ten parents were evaluated for eight traits of agronomic importance, including yield potential, in a replicated field trial. The ten parents were analyzed with 100 arbitrary decamer oligonucleotide primers and 22 microsatellite (simple sequence repeats, SSRs) primer sets via polymerase chain reaction (PCR). Out of the 100 random primers used, 74 were informative and amplified 202 non-redundant bands (variants) with a mean of 2.73 bands per polymorphic primer. All 22 microsatellite primer sets representing 23 loci in the rice genome showed polymorphisms among the ten parents and revealed 90 alleles with an average of 3.91 per SSR locus. Cluster analysis based on Nei's genetic distance calculated from the 291 (202 RAPDs, 89 SSRs) non-redundant variants separated the ten parental lines into two major groups that corresponds to indica and japonica subspecies, which is consistent with the pedigree information. Strong heterosis was observed in hybrids for most of the traits examined. For the 43 diallel crosses (excluding 2 crosses not heading), yield potential, its components (including panicles per plant, spikelets per panicle and 1000-grain weight) and their heterosis in F₁ hybrids showed a significant positive correlation with genetic distance. When separate analyses were performed for the three subsets, yield potential and its heterosis showed significant positive correlations with genetic distance for the 15 indica x indica crosses and the 6 japonica x japonica crosses; however, yield potential and its heterosis were not correlated with genetic distance for the 22 indica x japonica crosses. Results indicated that genetic distance measures based on RAPDs and SSRs may be useful for predicting yield potential and heterosis of intra-subspecific hybrids, but not inter-subspecies hybrids.     

Development of EST SSRs in Finger Millet (Eleusine coracana ssp coracana) and their Transferability to Pearl Millet (Pennisetum glaucum)

EST-SSR markers were developed using sequence information from 1740 expressed sequence tags (ESTs) of finger millet available in the public domain. A set of 31 SSR markers were synthesized based on di, tri, tetra and penta-nucleotide repeat sequences. These were used for PCR analysis of 11 elite germplasm lines of finger millet of Indian and African origin. Out of 31 SSR markers, amplification products were obtained for 17 primer pairs. Of these nine were found polymorphic with two alleles per locus. These 17 SSR primer pairs were also tested for amplification in three varieties of pearl millet (Pennisetum glaucum) and 11 could be transferred to pearl millet. The informative EST SSR markers developed, can be used in finger millet as well as pearl millet genetic improvement projects.     

Synergistic effects of Trichoshield on enhancement of growth and resistance to downy mildew in pearl millet

Trichoshield, a talc formulation consisting of spores of Trichoderma harzianum, Trichoderma lignorum, Gliocladium virens and Bacillus subtilis was tested, following different application methods, for its ability to promote growth of pearl millet plants and to induce resistance to downy mildew of pearl millet. Under laboratory conditions, trichoshield seed treatment enhanced seed germination and seedling vigor of pearl millet significantly over the control; under greenhouse conditions vegetative growth parameters like height, fresh and dry weight, leaf area and number of tillers were significantly enhanced over the control: Trichoshield formulation offered greater protection against downy mildew in comparison with individual strains of T. harzianum, T. lignorum, G. virensand B. subtilis. Among the methods of application, foliar spray was found to be a more efficient delivery method than seed treatment or slurry treatment. Combinations of foliar spray with seed treatment and slurry treatment produced the same effect as foliar spray alone. Under field conditions, trichoshield treatment enhanced reproductive parameters like number of earheads, length and girth of earheads, 1000 seed weight and yield significantly over the control. Days required for 50% flowering was reduced by 4 days compared to the control. Yield enhancement of 28% over the control was highly significant. Trichoshield treatment offered protection ranging from 52 to 71% under field conditions, depending on the application method. However, the chemical fungicide metalaxyl Apron provided the highest protection against downy mildew, both under greenhouse and field conditions.     

Studies on potassium release in an inceptisol soil (Holambi Series) at the minimum level of exchangeable potassium

Summary Ammonium acetate extractable potassium in the soil reached a minimum value of 6.8 mg K/100g soil after 14 crops of wheat and pearl millet in the field without applying any potassium fertilizer. At this level of ammonium acetate extractable K both wheat and pearl millet utilized about, 90 per cent of the total K from non-exchangeable sources. Wheat and pearl millet were grown in this soil in the greenhouse at different levels of K. At K₀ level wheat utilized 86 per cent of the total K uptake from the non-exchangeable source and pearl millet, 95 per cent. At K₁ level, wheat utilized only 19 per cent but at higher levels of K, there was build up in the K status of soils. In the case of pearl millet at K₁, K₂ and K₃ levels 59, 13 and 22 per cent of total uptake were contributed by non-exchangeable forms. The total K uptake by pearl millet was more than double that by wheat. Plant analysis showed that 83 per cent of the total K in wheat was contained in the shoot portion and the rest in the roots. The corresponding figures for pearl millet were 94 and 6 per cent.     

Effect of the Duration of the Vegetative Phase on Shoot Growth, Development and Yield in Pearl Millet (Pennisetum americanum (L.) Leeke)

Craufurd, P. Q. and Bidinger, F. R. 1988. Effect of the durationof the vegetative phase on shoot growth, development and yieldin pearl millet (Pennisetum americanum (L.) Leeke).–J.exp. Bot. 38: 124–139 The duration of the vegetative phase (DVP) in millet, whichis the major cause of variation in the crop duration, has markedeffects on the number of productive tillers per plant and onmainshoot (MS) and tiller grain yield. Daylength extensionswere used to vary the DVP and the effect on factors affectingpanicle (tiller) number per plant and panicle yield examinedin millet hybrid 841A x J104, grown in the field at Hyderabad,India. Tiller appearance, shoot leaf appearance and leaf area,and stem and panicle growth, in both MS and primary tillers(PTs), were monitored at frequent intervals over the season.At maturity grain yield per shoot was measured The concept of thermal time was used to describe shoot development.The rates of tiller appearance and shoot leaf appearance werelinearly related to thermal time and were not affected by DVPtreatments. The duration of the growth phase from panicle initiationto flowering (GS2) and from flowering to maturity (GS3) was320 and 390 degree days (°Cd), respectively. There was nodifference in rates of leaf or tiller appearance or developmentbetween MS and PTs. Tiller appearance, tiller leaf appearanceand tiller apical development all ceased at the same time inthe later initiated PTs, approximately 550 °Cd from sowing,shortly after rapid stem growth had begun. Tillers that didnot survive were all vegetative or in the early stages of reproductivedevelopment at this time The rate of accumulation of dry matter per plant was similarin all DVP treatments, but in the longer DVP treatments a greaterproportion of the dry matter was partitioned to the MS. Mainshootstem and panicle growth rates were increased by a longer DVP,as was grain yield on the MS, and these were related to increasedMS leaf area. Concurrently, growth rates and yields in laterinitiated tillers were reduced in relation to their leaf areas.Stem growth rate was proportionately increased more than paniclegrowth rate in the longer DVP treatments and this, combinedwith a longer duration of stem growth, resulted in greater stemdry matter at maturity and, therefore, in reduced harvest index.     

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F₇ Recombinant Inbred Lines (RILs) from cross H 77/833-2 × PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available.     

Development and characterization of twenty-five new polymorphic microsatellite markers in proso millet (Panicum miliaceum L.)

Millets such as proso millet have excellent nutritional properties and could become a basic resource for crop breeding programs and food diversification. In this study, 25 polymorphic microsatellite markers were developed and characterized through construction of an SSR-enriched library from genomic DNA of proso millet (Panicum miliaceum L.). In total, 110 alleles were detected, with an average of 4.4 alleles per locus. Values of major allele frequency (M _AF ) and expected heterozygosity (H _E ) ranged from 0.36 to 0.98 (mean = 0.73) and from 0.04 to 0.74 (mean = 0.37), respectively. The mean genetic similarity coefficient was 0.3711, indicating that among 50 accessions of proso millet there was wide genetic variation. The newly developed microsatellite markers should be useful tools for assessing genetic diversity, understanding population structure, and breeding of proso millet.     

Linkage relationships among molecular markers and storage root traits of carrot (Daucus carota L. ssp. sativus)

 A 109-point linkage map consisting of three phenotypic loci (P ₁, Y ₂, and Rs), six restriction fragment length polymorphisms (RFLPs), two random amplified polymorphic DNAs (RAPDs), 96 amplified fragment length polymorphisms (AFLPs), and two selective amplification of microsatellite polymorphic loci (SAMPL) was constructed for carrot (Daucus carota L. ssp. sativus; 2n=2x=18). The incidence of polymorphism was 36% for RFLP probes, 20% for RAPD primers, and 42% for AFLP primers. The overall incidence of disturbed segregation was 18%. Linkage relationships at a LOD score of 4.0 and θ=0.25 indicated 11 linkage groups. The total map length was 534.4 cM and the map was clearly unsaturated with markers spaced at 4.9 cM. AFLP P6B15 was 1.7 cM from P ₁, AFLP P1B34 was 2.2 cM from Y ₂, and AFLP P3B30XA was 8.1 cM from Rs. Received: 2 September 1998 / Accepted: 28 November 1998     

Variation in response of accessions of minor millets,Pennisetum americanum (L.) Leeke (pearl millet) and Eleusine coracana (L.) Gaertn (finger millet), and Eragrostis tef (Zucc.) Trotter (tef) to salinity in early seedling growth

The response to increasing NaCl concentration of seedlings of 25 accessions of Ethiopian land races of each of Pennisetum americanum (L.) Leeke (pearl millet) and Eleusine coracana (L.) Gaertn (finger millet), and 15 accessions of Eragrostis tef (Zucc.) Trotter (tef), was examined after two week's growth in NaCl solution culture. Although increasing NaCl concentration significantly reduced seedling root lengths, there was considerable variation within, and between accessions within each species.Analysis based upon a non-linear least square inversion method, using root length data, revealed significant differences in accessions of P. americanum and E. tef on the basis of the estimated salinity threshold, C _t , the NaCl concentrations at which root length begins to decrease. C _t did not differ significantly between E. coracana accessions. Estimates of C₅₀ and C₀, mininum concentrations causing a 50% decrease in root length, and zero root growth respectively, revealed differences between and within accessions for all three species. Overall, finger millet was more tolerant than tef, which was more tolerant than pearl millet. There is clear evidence that differences in tolerance are genetically based from broad sense heritability estimates.     

DNA fingerprinting detects genetic variability in the pearl millet downy mildew pathogen (Sclerospora graminicola)

Genetic variability in six host genotype-specific pathotypes of pearl millet downy mildew pathogen S. graminicola was studied at the molecular level using mini- and micro-satellites. Our results indicated that microsatellites (GAA)₆, (GACA)₄, and especially (GATA)₄ were quite informative and showed high levels of polymorphism among the pathotypes. The six pathotypes could be classified into five groups based on the cluster analysis of their genetic similarities, thereby confirming the existence of distinct host genotype-specific virulence in S. graminicola pathotypes. We demonstrate, for the first time, the use of DNA fingerprinting to detect genetic variation in downy mildew fungus of pearl millet.     

Growth and Photosynthetic Characteristics in Pearl Millet under Water Stress and Different Potassium Supply

Influence of supra-optimal concentrations of K on growth, water relations, and photosynthetic capacity in pearl millet under severe water deficit conditions was assessed in a glasshouse. Nineteen-days-old plants of two lines, ICMV-94133 and WCA-78, of Pennisetum glaucum (L.) R.Br. were subjected for 30 d to 235.0, 352.5, and 470.0 mg(K) kg^–1(soil) and two water regimes (100 and 30 % field capacity). Increasing K supply did not alleviate the effect of water deficit on the growth of two lines of pearl millet since additional amount of K in the growth medium had no effect on shoot dry mass, relative growth rate, plant leaf area, net assimilation rate, or leaf area ratio, although there was significant effect of drought stress on these variables. Soil moisture had a significant effect on net photosynthetic rate (P _N), transpiration rate, stomatal conductance, and water use efficiency of both pearl millet lines, but there was no significant effect of varying K supply on these variables. In WCA-78 an ameliorative effect of increasing supply of K on P _N was observed under water deficit. Chlorophyll (Chl) a and b contents increased significantly in both lines with increase in K supply under well watered conditions, but under water deficit they increased only in ICMV-94133. Chl a/b ratios were reduced significantly in WCA-78 with increasing K supply under both watering regimes, but by contrast, in ICMV-94133 this variable was decreased only under water stress. Leaf water potential and osmotic potential of both lines decreased significantly with the imposition of drought. Leaf pressure potential in both lines increased with increase in K supply under water stress. Contents of total free amino acids in the leaves of both pearl millet lines increased significantly with increase in K supply under water stress. Potassium supply had no effect on leaf soluble sugars or soluble proteins. Considerable osmotic adjustment occurred in pearl millet plants experiencing water deficit under high K supply.     

Mitochondrial DNA Polymorphisms Revealed by RAPD Assays Distinguish the Male-sterile and Male-fertile Cytoplasms in Pearl Millet

Diversification of cytoplamic male sterile (CMS) sources is of considerable significance in pearl millet, considering that almost all the commercially cultivated hybrids, particularly in India, are based on a single CMS source, A₁. We analyzed the mitochondrial DNA (mtDNA) polymorphisms among five pearl millet CMS sources (A₁ to A₅) and a male-fertile maintainer (B) line, all in an isonuclear background. Analysis using 21 random primers led to identification of polymorphic bands specific to the A₁, A₂, A3 and A₅ CMS lines. Two RAPD primers, OP-G12 and OP-G19, in combination were able to distinguish all the male-sterile and male-fertile cytoplasms. Highly effective for this purpose also were four RAPD markers, OP-B7, OP-D8, OP-F10 and OP-G12. Cluster analysis, followed by bootstrap analysis, of the mtDNA dataset revealed two distinct clusters: cluster-I comprising the A₁, A₂, A₃ CMS lines and the male-fertile line, and cluster-II comprising the A₄ and A₅ CMS lines.     

An RFLP-based genetic map of pearl millet (Pennisetum glaucum)

Analysis of a sample of diverse pearl millet genotypes with 200 genomic DNA probes revealed this crop species to be extremely polymorphic. Among these genotypes, 85% of probes detected polymorphism using only two restriction enzymes, with an average pair-wise polymorphism between all of the probe-enzyme combinations of 56%. Two crosses were employed to construct an RFLP-based genetic map. In an intervarietal F₂ population, derived from a single F₁ plant, 181 loci were placed on a linkage map. The total length of this map, which comprised seven linkage groups, was 303 cM and the average map distance between loci was about 2 cM, although a few intervals in excess of 10 cM were present at the ends of a few linkage groups. Very few clones, including those which hybridized to more than one copy, detected more than one locus in the pearl millet genome. The analysis was complicated initially because 83 of the 181 loci mapped to a single linkage group. Analysis of a second cross identified a probable translocation breakpoint in the middle of this large linkage group.     

Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [<Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv.]

The unavailability of microsatellite markers and saturated genetic linkage map has restricted the genetic improvement of foxtail millet [Setaria italica (L.) P. Beauv.], despite the fact that in recent times it has been documented as a new model species for biofuel grasses. With the objective to generate a good number of microsatellite markers in foxtail millet cultivar ‘Prasad’, 690 clones were sequenced which generated 112.95 kb high quality sequences obtained from three genomic libraries each enriched with different microsatellite repeat motifs. Microsatellites were identified in 512 (74.2%) of the 690 positive clones and 172 primer pairs (pp) were successfully designed from 249 (48.6%) unique SSR-containing clones. The efficacies of the microsatellite containing genomic sequences were established by superior primer designing ability (69%), PCR amplification efficiency (85.5%) and polymorphic potential (52%) in the parents of F₂ mapping population. Out of 172 pp, functional 147 markers showed high level of cross-species amplification (~74%) in six grass species. Higher polymorphism rate and broad range of genetic diversity (0.30–0.69 averaging 0.58) obtained in constructed phylogenetic tree using 52 microsatellite markers, demonstrated the utility of markers in germplasm characterizations. In silico comparative mapping of 147 foxtail millet microsatellite containing sequences against the mapping data of sorghum (~18%), maize (~16%) and rice (~5%) indicated the presence of orthologous sequences of the foxtail millet in the respective species. The result thus demonstrates the applicability of microsatellite markers in various genotyping applications, determining phylogenetic relationships and comparative mapping in several important grass species.