Pathogenic Variation in the Pearl Millet Blast Pathogen Magnaporthe grisea and Identification of Resistance to Diverse Pathotypes

Identification of genes controlling compatible and incompatible reactions of pearl millet (Pennisetum glaucum) against blast (Magnaporthe grisea) pathogen through RNA-Seq

Blast [Magnaporthe grisea (Herbert) Barr] is an economically important disease in Asian pearl millet production ecologies. The recurrent occurrence of blast in the past one decade has caused enormous strain on grain and forage production. Identification of resistance genes is an important step to develop durable varieties. The present study is the first attempt to use RNA-Seq to investigate the transcript dynamics in a pearl millet inbred ICMB 93333, which had a unique differential reaction to two isolates-Pg 45 (avirulent) and Pg 174 (virulent) of M. grisea. The inbred was inoculated by both isolates and samples taken at six different time intervals for genome-wide RNA-Seq experiment. The transcriptome results revealed the differential expression of more than 2,300 genes. The time-specific comparison showed activation or repression of specific genes in various pathways. Genes and transcriptions factors related to pathogenesis-related proteins, reactive oxygen species generating and its scavenging genes, cell wall defense, primary and secondary metabolic pathways, and signaling pathways were identified by comparing the host-plant compatible and incompatible interactions. The genes identified from this experiment could be useful to understand the host-plant resistance and design novel strategies to manage blast disease in pearl millet.

Genetic insights in pearl millet breeding in the genomic era: challenges and prospects

Pearl millet, a vital staple food and an important cereal, is emerging as crop having various end-uses as feed, food as well as fodder. Advancement in high-throughput sequencing technology has boosted up pearl millet genomic research in past few years. The available draft genome of pearl millet providing an insight into the advancement of several breeding lines. Comparative and functional genomics have untangled several loci and genes regulating adaptive and agronomic traits in pearl millet. Additionally, the knowledge achieved has far away from being applicable in real breeding practices. We believe that the best path ahead is to adopt genome-based approaches for tailored designing of pearl millet as multi-functional crop with outstanding agronomic traits for various end uses. Presently review highlight several novel concepts and techniques in crop breeding, and summarize the recent advances in pearl millet genomic research, peculiarly genome-wide association dissections of several novel alleles and genes for agronomically important traits.

Pearl Millet Blast Pathogen Virulence Study and Identification of Resistance Donors on Virulent Isolate

Pearl Millet leaf Blast caused by Pyricularia grisea [teleomorph: Magnaporthe grisea], is spreading at an alarming rate in the major Pearl millet growing geographies of India effecting grain yield and green fodder yield. Blast isolates collected from Jaipur, Alwar and Toopran regions of India and virulence study conducted to identify the most virulent isolate among the three isolates. Artificial screening for Blast conducted on a raised bed method utilising uniform Blast Nursery (UBN) method. Eleven Pearl Millet genotypes (ICMB01333, ICMB03444, ICMB03555, ICMB06111, ICMB95444, ICMB11666, ICMB14333, ICMB14666, ICMB97111, ICMR12888 and ICMR06444) were screened with three blast isolates utilising artificial screening method. Among the eleven genotypes, ten genotypes were showing susceptible to Jaipur isolate indicating that the Jaipur isolate having highest virulence among the three isolates. To identify Blast resistant donors for Jaipur isolate, a set of 93 genotypes containing of 45 maintainer lines and 48 restorer lines were screened under both UBN and field conditions (Jaipur, Rajasthan). Among all the lines evaluated, five lines are showing resistant reaction for Jaipur isolate with disease score less than 1.9. ICMR06444 from restorer background and IC414K14B5, IC594K16B5, RBB037 and IC6912K18B from maintainer background are identified as resistant lines. Identified lines can be utilised in pearl millet hybrid breeding programme.

Deciphering Genotype-By-Environment Interaction for Target Environmental Delineation and Identification of Stable Resistant Sources Against Foliar Blast Disease of Pearl Millet

Once thought to be a minor disease, foliar blast disease of pearl millet, caused by Magnaporthe grisea, has recently emerged as an important biotic constraint for pearl millet production in India. The presence of a wider host range as well as high pathogenic heterogeneity complicates host-pathogen dynamics. Furthermore, environmental factors play a significant role in exacerbating the disease severity. An attempt was made to unravel the genotype-by-environment interactions for identification and validation of stable resistant genotypes against foliar blast disease through multi-environment testing. A diversity panel consisting of 250 accessions collected from over 20 different countries was screened under natural epiphytotic conditions in five environments. A total of 43 resistant genotypes were found to have high and stable resistance. Interestingly, most of the resistant lines were late maturing. Combined ANOVA of these 250 genotypes exhibited significant genotype-by-environment interaction and indicated the involvement of crossover interaction with a consistent genotypic response. This justifies the necessity of multi-year and multi-location testing. The first two principal components (PCs) accounted for 44.85 and 29.22% of the total variance in the environment-centered blast scoring results. Heritability-adjusted genotype plus genotype × environment interaction (HA-GGE) biplot aptly identified "IP 11353" and "IP 22423, IP 7910 and IP 7941" as "ideal" and "desirable" genotypes, respectively, having stable resistance and genetic buffering capacity against this disease. Bootstrapping at a 95% confidence interval validated the recommendations of genotypes. Therefore, these genotypes can be used in future resistance breeding programs in pearl millet. Mega-environment delineation and desirability index suggested Jaipur as the ideal environment for precise testing of material against the disease and will increase proper resource optimization in future breeding programs. Information obtained in current study will be further used for genome-wide association mapping of foliar blast disease in pearl millet.

Genetic Gains in Pearl Millet in India: Insights Into Historic Breeding Strategies and Future Perspective

Pearl millet (Pennisetum glaucum R. Br.) is an important staple and nutritious food crop in the semiarid and arid ecologies of South Asia (SA) and Sub-Saharan Africa (SSA). In view of climate change, depleting water resources, and widespread malnutrition, there is a need to accelerate the rate of genetic gains in pearl millet productivity. This review discusses past strategies and future approaches to accelerate genetic gains to meet future demand. Pearl millet breeding in India has historically evolved very comprehensively from open-pollinated varieties development to hybrid breeding. Availability of stable cytoplasmic male sterility system with adequate restorers and strategic use of genetic resources from India and SSA laid the strong foundation of hybrid breeding. Genetic and cytoplasmic diversification of hybrid parental lines, periodic replacement of hybrids, and breeding disease-resistant and stress-tolerant cultivars have been areas of very high priority. As a result, an annual yield increase of 4% has been realized in the last three decades. There is considerable scope to further accelerate the efforts on hybrid breeding for drought-prone areas in SA and SSA. Heterotic grouping of hybrid parental lines is essential to sustain long-term genetic gains. Time is now ripe for mainstreaming of the nutritional traits improvement in pearl millet breeding programs. New opportunities are emerging to improve the efficiency and precision of breeding. Development and application of high-throughput genomic tools, speed breeding, and precision phenotyping protocols need to be intensified to exploit a huge wealth of native genetic variation available in pearl millet to accelerate the genetic gains.

Genetic Gains in Pearl Millet in India: Insights Into Historic Breeding Strategies and Future Perspective

Pearl millet (Pennisetum glaucum R. Br.) is an important staple and nutritious food crop in the semiarid and arid ecologies of South Asia (SA) and Sub-Saharan Africa (SSA). In view of climate change, depleting water resources, and widespread malnutrition, there is a need to accelerate the rate of genetic gains in pearl millet productivity. This review discusses past strategies and future approaches to accelerate genetic gains to meet future demand. Pearl millet breeding in India has historically evolved very comprehensively from open-pollinated varieties development to hybrid breeding. Availability of stable cytoplasmic male sterility system with adequate restorers and strategic use of genetic resources from India and SSA laid the strong foundation of hybrid breeding. Genetic and cytoplasmic diversification of hybrid parental lines, periodic replacement of hybrids, and breeding disease-resistant and stress-tolerant cultivars have been areas of very high priority. As a result, an annual yield increase of 4% has been realized in the last three decades. There is considerable scope to further accelerate the efforts on hybrid breeding for drought-prone areas in SA and SSA. Heterotic grouping of hybrid parental lines is essential to sustain long-term genetic gains. Time is now ripe for mainstreaming of the nutritional traits improvement in pearl millet breeding programs. New opportunities are emerging to improve the efficiency and precision of breeding. Development and application of high-throughput genomic tools, speed breeding, and precision phenotyping protocols need to be intensified to exploit a huge wealth of native genetic variation available in pearl millet to accelerate the genetic gains.

Elucidation of genetic relatedness of Magnaporthe grisea, an incitent of pearl millet blast disease by molecular markers associated with virulence of host differential cultivars

In recent years, blast disease caused by Magnaporthe grisea, an ascomycete fungus is becoming a serious threat to pearl millet crop in India and worldwide. Due to the increase in virulent races of pathogen, blast disease management strategies seemed to be very limited. Hence, unraveling the occurrence of blast isolates across India and understanding their virulence and genetic relatedness using molecular markers are the key objectives of this study. From Farmer's field survey we have evidenced variability in blast pathogen across India by recording 10.6 to 7.9 disease severities. A fair to good variation in cultural and conidial characters were also noticed for 17 field isolates. The identity of 17 isolates was confirmed as Magnaporthe grisea by internal transcribed spacer (ITS) region. Based on 12 host differential virulence reactions, five isolates BgKMg1, BdmMg2, MtgMg11, JprMg16 and JmnMg17 recorded highly susceptible (>5 grade) to nine differentials used in the study. While, host differentials ICMB95444, ICMR06222, ICMR11003, IP21187 and ICMV155 found effective for screening virulence of blast disease. Furthermore, genetic relatedness assessed by ITS, inter simple sequence repeats (ISSR) and simple sequence repeats (SSR) markers produced high degree of polymorphism and was able to distinguish the virulence pattern of 17 isolates that correlated with phenotypic screening. Among markers, clustering of isolates within groups was significantly different with remarkable genetic similarity coefficient and bootstrap values. Overall, these results confirm a significant morphological and genetic variation among 17 isolates, thereby helping to elucidate the virulence of pearl millet blast populations in India that could avoid breakdown of resistance and assist breeding improved pearl millet cultivars.

Tapping Pennisetum violaceum, a Wild Relative of Pearl Millet (Pennisetum glaucum), for Resistance to Blast (caused by Magnaporthe grisea) and Rust (caused by Puccinia substriata var. indica)

Blast (Magnaporthe grisea) and rust (Puccinia substriata var. indica) are the two important foliar diseases of pearl millet (Pennisetum glaucum (L.) R. Br.) that can be best managed through host plant resistance. For identification of diverse sources of blast and rust resistance, 305 accessions of Pennisetum violaceum, a wild relative of pearl millet, were screened under greenhouse conditions against five pathotype-isolates of M. grisea and a local isolate of P. substriata var. indica collected from ICRISAT farm, Patancheru, India. Based on the mean blast score (1 to 9 scale), 17 accessions (IP 21525, 21531, 21536, 21540, 21594, 21610, 21640, 21706, 21711, 21716, 21719, 21720, 21721, 21724, 21987, 21988, and 22160) were found resistant (score ≤3.0) to all five pathotypes, and 24 accessions were resistant to four pathotypes of M. grisea. As there was variability for rust resistance within some accessions, individual rust-resistant (<5% severity) plants from 17 accessions were selected, grown in pots and advanced to next generation by selfing, and rescreened for three to four generations following pedigree selection to develop rust-resistant genetic stocks. Single plant selections from nine accessions (IP 21629, 21645, 21658, 21660, 21662, 21711, 21974, 21975, and 22038) were found highly resistant to rust (0% rust severity) after four generations of pedigree selection and subsequent screening. Some of the blast-resistant accessions and rust-resistant genetic stocks are being utilized in a prebreeding program at ICRISAT for introgressing resistance genes from the wild into the parental lines of cultivated and potential pearl millet hybrids and varieties.

Genome Sequence of a Unique Magnaporthe oryzae RMg-Dl Isolate from India That Causes Blast Disease in Diverse Cereal Crops, Obtained Using PacBio Single-Molecule and Illumina HiSeq2500 Sequencing

The whole-genome assembly of a unique rice isolate from India, Magnaporthe oryzae RMg-Dl that causes blast disease in diverse cereal crops is presented. Analysis of the 34.82 Mb genome sequence will aid in better understanding the genetic determinants of host range, host jump, survival, pathogenicity, and virulence factors of M. oryzae.

Selection of Host Differentials for Elucidating Pathogenic Variation in Magnaporthe grisea Populations Adapted to Finger Millet (Eleusine coracana)

Blast, caused by Pyricularia grisea (teleomorph: Magnaporthe grisea), is the most devastating disease of finger millet affecting production, utilization, and trade in Africa and Southeast Asia. An attempt was made to select a set of putative host differentials that can be used to determine virulence diversity in finger-millet-infecting populations of M. grisea. Thus, a differential set comprising eight germplasm accessions selected from finger millet core collection (IE 2911, IE 2957, IE 3392, IE 4497, IE 5091, IE 6240, IE 6337, and IE 7079) and a resistant ('GPU 28') and a susceptible ('VR 708') variety was developed. This differential set was used to study pathogenic variation in 25 isolates of M. grisea collected from Karnataka, Telangana, and Andhra Pradesh states in India. Based on the reaction (virulent = score ≥4 and avirulent = score ≤3 on a 1-to-9 scale) on host differentials, nine pathotypes were identified among 25 M. grisea isolates. Pathotype 9, represented by isolate Pg23 from Vizianagaram, was the most virulent because it could infect all of the host differentials except GPU 28. This study will be helpful in devising strategies for monitoring virulence change in M. grisea populations, and for identification of blast resistance in finger millet for use in disease resistance breeding programs.

Comparison of Pathogenic Variation among Phakopsora pachyrhizi Isolates Collected from the United States and International Locations, and Identification of Soybean Genotypes Resistant to the U.S. Isolates

A major constraint in breeding for resistance to soybean rust has been the virulence diversity in Phakopsora pachyrhizi populations. In greenhouse experiments, reactions of 18 soybean genotypes to 24 U.S. isolates from 2007 and 2008 and 4 foreign isolates were compared. Reactions of four differentials (Rpp1 to Rpp4) to these U.S. isolates were also compared with reactions to nine foreign isolates and three U.S. isolates from 2004. Principal component analysis (PCA) of the reaction types grouped the U.S. isolates into a single virulence group, whereas each of the foreign isolates had a unique virulence pattern. In another experiment, reactions of 11 differentials to the 24 U.S. isolates were compared and significant interactions (P < 0.001) were found between the isolates and host genotypes for rust severity and uredinia densities. PCA of these two measures of disease placed the 24 isolates into seven or six aggressiveness groups, respectively. In a third experiment, evaluation of 20 soybean genotypes for resistance to the previously established aggressive groups identified 10 genotypes resistant to isolates representing most of the groups. This study confirmed the pathogenic diversity in P. pachyrhizi populations and identified soybean germplasm with resistance to representative U.S. isolates that can be used in breeding.

Identification of Blast Resistance in a Core Collection of Foxtail Millet Germplasm

Blast, also known as leaf spot, caused by Pyricularia grisea (teleomorph: Magnaporthe grisea), is a serious disease affecting both forage and grain production in foxtail millet in India. For the identification of new and diverse sources of blast resistance, a foxtail millet core collection comprising 155 accessions was evaluated against the Patancheru isolate (Fx 57) of M. grisea. In a field screen during 2009 and 2010, 21 accessions were identified with neck and head blast resistance against Fx 57. In a greenhouse screen, 11 of the 155 accessions exhibited seedling leaf blast resistance to the same isolate. Further evaluation of the selected 28 accessions (found resistant to neck and head blast under field conditions during 2009 and 2010 or leaf blast in the greenhouse screen) against four M. grisea isolates (Fx 57, Fx 58, Fx 60, and Fx 62 from Patancheru, Nandyal, Vizianagaram, and Mandya, respectively) led to the identification of 16 accessions with leaf, sheath, neck, and head blast resistance to at least one isolate. Two accessions (ISe 1181 and ISe 1547) were free from head blast infection and showed resistance to leaf (score ≤3.0 on a 1-to-9 scale), neck, and sheath blast (score ≤2.0 on a 1-to-5 scale) against all four isolates. In addition, ISe 1067 and ISe 1575 also exhibited high levels of blast resistance. Blast-resistant accessions with superior agronomic and nutritional quality traits can be evaluated in multilocation yield trials before releasing them for cultivation to farmers.