Bioefficacy of certain chemical and biofungicides against Hypoxylon spp. causing wood rot disease in tea

Wood rot disease caused by Hypoxylon serpens is the most widespread and serious stem disease in tea. Among the 350 bacterial and 35 fungal biocontrol isolates collected from several tea growing regions of southern India, three bacterial isolates produced higher antagonistic potential against this fungal pathogen. Two of the efficient strains were identified as Bacillus sp. (HBCWR-3 and WR46-2) and third one was Pseudomonas sp. (WR5-4). In case of fungal biocontrol agents, the type culture Trichoderma viride procured from Microbial Type Culture Collection (MTCC) performed better in controlling the pathogen over T. harzianum. Five systemic fungicides, hexaconazole, carbendazim, tebuconazole, tridemorph, benomyl and a contact fungicide, copper oxychloride were evaluated for studying their bioefficacy against wood rot pathogen. In this study, benomyl 50% WP or copper oxychloride at the lowest concentration (0.01%) completely inhibited the growth of the fungus in vitro. Moreover, bioefficacy of certain plant aqueous extracts of Azadirachta indica, acetone extracts of Pongamia pinnata, Cinnamom, Artemisia nilagirica, Lantana camera, Ageratum conyzoides and a bryophyte, Heteroscyphus argutus were also studied against H. serpens. Among them, A. nilagirica followed by H. argutus and A. indica were effective in controlling the wood rot pathogen. In the case of liquid biofungicides tested, ‘Expel’ controlled the tea pathogen efficiently. The present study revealed that, chemical fungicide (Benomyl or copper oxychloride at 0.01%), botanical extracts at 10% (A. nilagirica, H. argutus, Azadirachta and ‘Expel’) and biocontrol agents (Bacillus sp., Pseudomonas sp. and T. viride) were effective in controlling wood rot pathogen under in vitro condition

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

Bioefficacy of efficient entomopathogenic fungus against branch canker pathogen (Macrophoma theicola) in tea plantations of southern India

Three branch canker pathogens, viz. NBCHE-6, UPA-61 and VPM were isolated from different tea growing districts of south India and four entomopathogenic fungus, viz. Beauveria bassiana, Paecilomyces lilacinus, Lecannicillium lecannii and Paecilomyces fumosoroseus were procured from the microbial type culture collection and gene bank (MTCC), Chandigarh. In vitro studies revealed that Beuveria bassiana showed highest antagonistic effect against NBCHE-6 (64.22) followed by Paecilomyces fumosoroseus against UPA-61(56.66). Paecilomyces lilacinus significantly controlled VPM (54.66), while Lecannicillium lecannii showed insignificantly control against VPM (47.33). While Beuveria bassiana and Paecilomyces lilacinus coiled around and shrink branch canker pathogen, Lecannicillium lecannii breaks into branch canker hyphae and Paecilomyces fumosoroseus produces more spore to kill branch canker. In culture filtrate studies, Paecilomyces fumosoroseus and Paecilomyces lilacinus showed maximum control of VPM (68.44) and UPA-61 (65.59). Beauveria bassiana also showed significant control of two isolates VPM and UPA-61 (54.44). Lecanniicillium lecannii showed least control of VPM (30.44). This study concludes that entomopathogens can significantly control branch canker pathogen (Macrophoma theicola)

QTL mapping of pearl millet rust resistance using an integrated DArT- and SSR-based linkage map

Rust, caused by the fungus Puccinia substriata var. indica, is one of the most important production constraints of pearl millet worldwide, leading to grain yield losses of up to 76 % as well as major losses in fodder yield and quality. Here, we report the development of a linkage map integrating Diversity Arrays Technology (DArT) markers and simple sequence repeat (SSR) markers, using this to identify quantitative trait loci (QTLs) for pearl millet rust resistance. Genotyping data from 256 DArT and 70 SSR markers on 168 F7 recombinant inbred lines from cross 81B-P6 × ICMP 451-P8 were used to construct a linkage map comprised of 286 loci (229 DArT and 57 SSR markers) spanning a total length of 740.3 cM (Haldane) with an average adjacent marker distance of 2.7 cM. Linkage group 7 (LG7) (153.5 cM) was the longest and LG6 the shortest (45.0 cM). The map was used to identify a major QTL for rust resistance with an LOD score of 27 on LG1, which explained 58 % of the observed phenotypic variation. In addition, two putative modifiers of small effect were detected, one each on LG4 and LG7. The novel rust resistance QTL identified on LG1 is thought to confer a durable slow-rusting phenotype, which is still effective in India more than 20 years after it was first deployed in the previously popular single-cross hybrid MH 179 (ICMH 451). The flanking markers reported here provide a framework for marker-assisted selection and possible future map-based cloning of this resistance gene

Deciphering Genomic Regions for High Grain Iron and Zinc Content Using Association Mapping in Pearl Millet

Micronutrient malnutrition, especially deficiency of two mineral elements, iron [Fe] and zinc [Zn] in the developing world needs urgent attention. Pearl millet is one of the best crops with many nutritional properties and is accessible to the poor. We report findings of the first attempt to mine favorable alleles for grain iron and zinc content through association mapping in pearl millet. An association mapping panel of 130 diverse lines was evaluated at Delhi, Jodhpur and Dharwad, representing all the three pearl millet growing agro-climatic zones of India, during 2014 and 2015. Wide range of variation was observed for grain iron (32.3–111.9 ppm) and zinc (26.6–73.7 ppm) content. Genotyping with 114 representative polymorphic SSRs revealed 0.35 mean gene diversity. STRUCTURE analysis revealed presence of three sub-populations which was further supported by Neighbor-Joining method of clustering and principal coordinate analysis (PCoA). Marker-trait associations (MTAs) were analyzed with 267 markers (250 SSRs and 17 genic markers) in both general linear model (GLM) and mixed linear model (MLM), however, MTAs resulting from MLM were considered for more robustness of the associations. After appropriate Bonferroni correction, Xpsmp 2261 (13.34% R2-value), Xipes 0180 (R2-value of 11.40%) and Xipes 0096 (R2-value of 11.38%) were consistently associated with grain iron and zinc content for all the three locations. Favorable alleles and promising lines were identified for across and specific environments. PPMI 1102 had highest number (7) of favorable alleles, followed by four each for PPMFeZMP 199 and PPMI 708 for across the environment performance for both grain Fe and Zn content, while PPMI 1104 had alleles specific to Dharwad for grain Fe and Zn content. When compared with the reference genome Tift 23D2B1-P1-P5, Xpsmp 2261 amplicon was identified in intergenic region on pseudomolecule 5, while the other marker, Xipes 0810 was observed to be overlapping with aspartic proteinase (Asp) gene on pseudomolecule 3. Thus, this study can help in breeding new lines with enhanced micronutrient content using marker-assisted selection (MAS) in pearl millet leading to improved well-being especially for women and children

Development of a Set of Chromosome Segment Substitution Lines in Pearl Millet [Pennisetum glaucum (L.) R. Br.]

The detection of minor quantitative trait loci (QTL) with conventional mapping populations can be complicated by the overshadowing effect of major QTL as well as by interactions between QTL. To overcome these constraints, we developed a set of chromosome segment substitution lines (CSSLs) by introgression of overlapping chromosome segments from 863B into ICMB 841 background for use in QTL detection, fine mapping, and trait mechanism studies, especially for complex traits. Since each CSSL carries one or a few donor segments in the genetic background of the recurrent genotype, the QTL interaction is confined to genes present on small homozygous substituted segments. Advanced generation backcross progenies (1492), expected to provide coverage across the mapped length of each of the seven pearl millet linkage groups (LGs), were genotyped at 74 marker loci [(48 simple sequence repeats (SSRs), 21 single strand conformation polymorphism-single nucleotide polymorphism (SSCP-SNP), and 5 sequence tagged sites (STSs)] identifying 124 segment introgression homozygotes (13 for LG1, 9 for LG2, 10 for LG3, 41 for LG4, 23 for LG5, 11 for LG6, and 17 for LG7). These CSSLs consisted of 1–3 homozygous introgression segments substituted from 863B in the genetic background of the recurrent parent ICMB 841 and among them, 54 represent unique lines with the donor chromosome segment averaging 100.69 cM. These CSSLs developed here provide a nearly ideal set of genetic stocks for mapping and fine mapping the multitude of traits for which their parents differ

Performance and Stability of Pearl Millet Varieties for Grain Yield and Micronutrients in Arid and Semi-Arid Regions of India

Pearl millet [Pennisetum glaucum (L.) R. Br.] is grown under both arid and semi-arid conditions in India, where other cereals are hard to grow. Pearl millet cultivars, hybrids, and OPVs (open pollinated varieties) are tested and released by the All India Coordinated Research Project on Pearl Millet (AICRP-PM) across three zones (A1, A, and B) that are classified based on rainfall pattern. Except in locations with extreme weather conditions, hybrids dominate pearl millet growing areas, which can be attributed to hybrid vigor and the active role of the private sector. The importance of OPVs cannot be ruled out, owing to wider adaptation, lower input cost, and timely seed availability to subsidiary farmers cultivating this crop. This study was conducted to scrutinize the presently used test locations for evaluation of pearl millet OPVs across India, identify the best OPVs across locations, and determine the variation in grain Fe and Zn contents across locations in these regions. Six varieties were evaluated across 20 locations in A1 and A (pooled as A) and B zones along with three common checks and additional three zonal adapted checks in the respective zones during the 2019 rainy season. Recorded data on yield and quality traits were analyzed using genotype main effects and genotype × environment interaction biplot method. The genotype × environment (G × E) interaction was found to be highly significant for all the grain yield and agronomic traits and for both micronutrients (iron and zinc). However, genotypic effect (G) was four (productive tillers) to 49 (grain Fe content) times that of G × E interaction effect for various traits across zones that show the flexibility of OPVs. Ananthapuramu is the ideal test site for selecting pearl millet cultivars effectively for adaptation across India, while Ananthapuramu, Perumallapalle, and Gurugram can also be used as initial testing locations. OPVs MP 599 and MP 600 are identified as ideal genotypes, because they showed higher grain and fodder yields and stability compared with other cultivars. Iron and zinc concentration showed highly significant positive correlation (across environment = 0.83; p < 0.01), indicating possibility of simultaneous effective selection for both traits. Three common checks were found to be significantly low yielders than the test entries or zonal checks in individual zones and across India, indicating the potential of genetic improvement through OPVs

Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers

Pearl millet [Pennisetum glaucum (L.) R. Br; also Cenchrus americanus (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-sequencing (GBS) markers can be used to build high-density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines ‘Tift 99D2B1’ and ‘Tift 454’. DNA from 186 RILs, the parents, and the F1 was used for 96-plex ApeKI GBS library development, which was further used for sequencing. The sequencing results showed that the average number of good reads per individual was 2.2 million, the pass filter rate was 88%, and the CV was 43%. High-quality GBS markers were developed with stringent filtering on sequence data from 179 RILs. The reference genetic map developed using 150 RILs contained 16,650 single-nucleotide polymorphisms (SNPs) and 333,567 sequence tags spread across all seven chromosomes. The overall average density of SNP markers was 23.23 SNP/cM in the final map and 1.66 unique linkage bins per cM covering a total genetic distance of 716.7 cM. The linkage map was further validated for its utility by using it in mapping quantitative trait loci (QTLs) for flowering time and resistance to Pyricularia leaf spot [Pyricularia grisea (Cke.) Sacc.]. This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community

Genomic-based-breeding tools for tropical maize improvement

Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail

Association analysis of low-phosphorus tolerance in West African pearl millet using DArT markers

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a food security crop in the harshest agricultural regions of the world. While low soil phosphorus (P) availability is a big constraint on its production, especially in West Africa (WA), information on genomic regions responsible for low-P tolerance in pearl millet is generally lacking. We present the first report on genetic polymorphisms underlying several plant P-related parameters, flowering time (FLO) and grain yield (GY) under P-limiting conditions based on 285 diversity array technology markers and 151 West African pearl millet inbred lines phenotyped in six environments in WA under both high-P and low-P conditions. Nine markers were significantly associated with P-related traits, nine markers were associated with FLO, whereas 13 markers were associated with GY each explaining between 5.5 and 15.9 % of the observed variation. Both constitutive and adaptive associations were observed for FLO and GY, with markers PgPb11603 and PgPb12954 being associated with the most stable effects on FLO and GY, respectively, across locations. There were a few shared polymorphisms between traits, especially P-efficiency-related traits and GY, implying possible colocation of genomic regions responsible for these traits. Our findings help bridge the gap between quantitative and molecular methods of studying complex traits like low-P tolerance in WA. However, validation of these markers is necessary to determine their potential applicability in marker-assisted selection programs targeting low-P environments, which are especially important in WA where resource-poor farmers are expected to be the hardest hit by the approaching global P crisis