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It is vital to screen the germplasm of crop plants for salt stress tolerance so as to utilize them in breeding programs. Accordingly, in the present study, twenty diverse inbred lines, parents of mapping populations of pearl millet were chosen to determine the phenotypic contrasts for seed yield, which can open the way for developing salt tolerance QTLs. Parents were grown in two summer seasons (late and early) with VPD ≥ 2 kPa, and one rainy season with VPD

Draft genome, 994 re-sequenced lines and GWAS for yield-traits provide a resource of genetics and genomics tools for pearl millet researchers and breeders. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users., Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users.

Pearl millet (Pennisetum glaucum (L.) R. Br.) is an important hybrid crop in India. However, to date limited pearl millet hybrid development has been undertaken in West Africa (WA), which is the center of pearl millet origin and diversity and where this crop is most important outside India. Using a diverse set of WA pearl millet germplasm, objectives of this study were to determine the superiority of population hybrids over open-pollinated varieties for agro-morphological and agronomic traits in WA pearl millet germplasm; and (ii) to derive strategies for pearl millet hybrid breeding in WA, based on quantitative-genetic parameters, combining ability and heterotic patterns among geographically close versus distant pearl millet populations. A 10 × 10 factorial mating design was performed with four parental OPVs from each of five WA countries. The 100 population hybrids and their parents were tested for 14 traits at six locations in one year, thereby using contrasting locations to indirectly sample the rainfall variability inherent to WA pearl millet production environments. Grain yield showed an average panmictic midparent heterosis (PMpH) of 16.7%, ranging from −26 to 73%. The mean grain yield of hybrids based on inter-country crosses did not differ significantly from intra-country crosses. Geographic distance between parents was positively correlated with hybrid grain yield (r = 0.31), but not with PMpH . Some crosses between accessions from Niger/Nigeria and Senegal were outstanding. Predictability of population hybrid performance for grain yield was moderate based on midparent values (r = 0.43) and slightly better based on general combining ability (GCA) (r = 0.56). Overall, pearl millet hybrid breeding in WA seems very promising, but there do not seem to be clear “natural” heterotic groups among WA pearl millet landraces. Such heterotic groups as the basis of sustainable hybrid breeding need rather to be created systematically, by building on existing combining ability patterns and aiming to maximize combining ability between the groups.

Phosphorus (P) deficiency at early seedling stages is a critical determinant for survival and final yield of pearl millet in multi-stress Sahelian environments. Longer roots and colonization with arbuscular mycorrhizal fungi (AMF) enhance P uptake and crop performance of millet. Assessing the genotypic variation of early mycorrhization and its effect on plant growth is necessary to better understand mechanisms of resistance to low soil P and to use them in breeding strategies for low P. Therefore, in this study, eight pearl millet varieties contrasting in low-P resistance were grown in pots under low P (no additional P supply) and high P (+ 0.4 g P pot−1) conditions, and harvested 2, 4, 6, and 8 weeks after sowing (WAS). Root length was calculated 2 WAS by scanning of dissected roots and evaluation with WinRhizo software. AM infection (%) and P uptake (shoot P concentration multiplied per shoot dry matter) were measured at each harvest. Across harvests under low P (3.3 mg Bray P kg−1), resistant genotypes had greater total root length infected with AMF (837 m), higher percentage of AMF colonization (11.6%), and increased P uptake (69.4 mg P plant−1) than sensitive genotypes (177 m, 7.1% colonization and 46.4 mg P plant−1, respectively). Two WAS, resistant genotypes were infected almost twice as much as sensitive ones (4.1% and 2.1%) and the individual resistant genotypes differed in the percentage of AMF infection. AMF colonization was positively related to final dry matter production in pots, which corresponded to field performance. Early mycorrhization enhanced P uptake in pearl millet grown under P-deficient conditions, with the genotypic variation for this parameter allowing selection for better performance under field conditions.

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross&mdash, RSG04008-6 (stay-green) &times, J2614-11 (moderately senescent). The fine-mapping population with 1894 F2 was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F4 generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing&mdash, Single Nucleotide Polymorphism (GBS&ndash, SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (Sobic.010G202700), NBS-LRR protein (Sobic.010G205600), ankyrin-repeat protein (Sobic.010G205800), senescence-associated protein (Sobic.010G270300), WD40 (Sobic.010G205900), CPK1 adapter protein (Sobic.010G264400), LEA2 protein (Sobic.010G259200) and an expressed protein (Sobic.010G201100). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)&ndash, PCR.

Shoot fly is a major insect pest of sorghum damaging early crop growth, establishment and productivity. Host plant resistance is an efficient approach to minimize yield losses due to shoot fly infestation. Seedling leaf blade glossiness and trichome density are morphological traits associated with shoot fly resistance. Our objective was to identify and evaluate QTLs for glossiness and trichome density using- i) 1894 F2s, ii) a sub-set of 369 F2-recombinants, and iii) their derived 369 F2:3 progenies, from a cross involving introgression lines RSG04008-6 (susceptible) × J2614-11 (resistant). The QTLs were mapped to a 37–72 centimorgan (cM) or 5–15 Mb interval on the long arm of sorghum chromosome 10 (SBI-10L) with flanking markers Xgap001 and Xtxp141. One QTL each for glossiness (QGls10) and trichome density (QTd10) were mapped in marker interval Xgap001-Xnhsbm1044 and Xisep0630-Xtxp141, confirming their loose linkage, for which phenotypic variation accounted for ranged from 2.29 to 11.37 % and LOD values ranged from 2.03 to 24.13, respectively. Average physical map positions for glossiness and trichome density QTLs on SBI-10 from earlier studies were 4 and 2 Mb, which in the present study were reduced to 2 Mb and 800 kb, respectively. Candidate genes Glossy15 (Sb10g025053) and ethylene zinc finger protein (Sb10g027550) falling in support intervals for glossiness and trichome density QTLs, respectively, are discussed. Also we identified a sub-set of recombinant population that will facilitate further fine mapping of the leaf blade glossiness and trichome density QTLs on SBI-10.

Pearl millet [Pennisetum glaucum (L.) R. Br.] open-pollinated varieties, which are the predominant cultivars, have never been systematically evaluated for adaptation to low-soil phosphorus (P), a major constraint on pearl millet production in West Africa (WA). We evaluated grain yield (GY), flowering time (FLO), harvest index (HI), and residual grain yields (RGY) of 102 open-pollinated varieties from WA under low-P (−P) and high-P (+P) field conditions in six environments of WA. In addition, PE-related traits of the varieties were evaluated at early growth stage in a pot experiment. Significant genetic variation was observed for GY, FLO, HI and PE-related traits. P-efficient varieties had higher yield under −P conditions. Varietal performance under −P varied across environments depending on FLO, relative flowering delay under −P (FD) and RGY measured in the field. Low-P-susceptible varieties had higher FLO, lower HI than low-P-tolerant varieties. Response to direct selection under −P field conditions was 20.1 g m−2, whereas indirect selection response under +P was 16.3 g m−2. Selection under −P field conditions while taking into account seasonal variations for FLO, FD and PE is expected to be important for improving GY specifically targeting −P environments in WA.

The parasitic weed Striga hermonthica hampers the production of sorghum, the most important cereal crop in Eritrea. This weed has a complex mode of infestation that adapts to many hosts and environments, complicating conventional breeding for resistance, which is the only form of crop improvement available to Eritrean breeders, but has failed. This study aimed at improving resistance against this parasite by transferring 5 Striga resistant Quantitative Trait Loci (QTLs) from resistance donor N13 to Striga susceptible Farmer-Preferred Sorghum Variety (FPSV) Hugurtay from Eritrea. The method involved backcrossing using marker-assisted selection (MAS) and evaluation of the best introgressed lines for Striga resistance in artificially infested fields. Foreground selection was performed with up to 11 polymorphic simple sequence repeat (SSR) markers linked to Striga resistance QTLs, while background selection was conducted in the BC 3 F 2 generation with 27 polymorphic unlinked SSR markers to identify the best recovery of the recurrent parent (RP) genetic background. Out of 84 BC 3 F 3 lines, L2P3-B, L1P5-A and L2P5P35 performed best with respect to both grain yield and reduced Striga infestation. These lines were more resistant to Striga than Hugurtay, but less resistant than N13. The three lines yielded twice as much as N13, with Area Under Striga Number Progression Curve (AUSNPC) values on average 18% higher than that of N13 and 38% lower than that of Hugurtay. This suggests that the introgressed QTLs conferred significant Striga resistance and yield advantage to these BC 3 F 3 backcross progenies under Striga pressure. These lines have good potential for future release and demonstrate that when MAS is available to conventional breeders, even in countries with no genotyping facilities, it is a useful tool for enhancement, expediency and precision in crop improvement.

Pearl millet [Pennisetum glaucum (L.) R. Br.] was domesticated in Sahelian West Africa. This highly outcrossing crop is one of the most important staple cereals in the semiarid tropics, adapted to very harsh rain-fed conditions. Agro-morphological characterization of local germplasm is very important to better understand existing diversity, ease targeted genetic broadening of breeding populations, and potentially link this knowledge to genotypic information. The objectives of our study were to (i) characterize West and Central African (WCA) pearl millet accessions based on their agro-morphological traits; (ii) evaluate the possibility to group accessions based on their agro-morphological characteristics; (iii) determine geographic patterns of phenotypic differentiation; and (iv) derive conclusions for pearl millet improvement in WCA. A total of 360 early-tomedium maturity accessions were phenotyped for 12 agro-morphological traits at six environments in WCA. Wide ranges of all observed traits indicated a high diversity of the tested accessions. Principal component analysis revealed very large diversity within individual countries, especially within Mali and Burkina Faso. Some limited grouping of accessions from Niger, Senegal, Cameroon, Morocco, and Mauritania was observed for individual principal component axes. Geographical differentiation and country differences were detected for several traits. The results and data presented in our study reflect WCA pearl millets’ tremendous diversity and adaptability to a wide range of environments and give a sound basis for breeders to select and utilize this germplasm to serve the manifold needs of WCA pearl millet farmers.

Pearl millet [Pennisetum glaucum (L.) R. Br] production on the acid sandy Sahelian soils in West Africa (WA) is severely limited by low plant-available phosphorus (P) in addition to erratic rainfall. We sought to examine the genetic variability for P uptake and P utilization efficiency in 180 WA pearl millet inbred lines or subsets thereof under low (LP) and high P (HP) conditions in one field and two pot experiments, determine the relationships among the measured traits and grain yield under field conditions at three other independent WA sites, and identify potential secondary selection traits for improving grain yield under LP. We observed genetic variation for P uptake and utilization in both seedling and mature plants. P utilization efficiency increased under LP conditions. Total P uptake was more important for grain production than P utilization under LP field conditions (r = 0.57*** vs r = 0.30***). The estimated response to indirect selection was positive for most of the measured morphological and P-efficiency parameters. We conclude that both seedling and mature plant traits are potentially useful as secondary traits in selection of pearl millet for low-P adaptation. These results should be validated using heterozygous pearl millet genetic materials. Ultimately, pearl millet breeding activities for low P tolerance in WA should be integrated with other system-oriented research such as nutrient cycling, intercropping or rotations with legumes, better crop-tree-livestock integration, and modest applications of locally available rock phosphate.

Background Pearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production through hybrid breeding. Cytoplasmic male sterility (CMS) and the corresponding nuclear fertility restoration / sterility maintenance genes (Rfs) are essential tools for economic hybrid seed production in pearl millet. Mapping the Rf genes of the A4 CMS system in pearl millet would enable more efficient introgression of both dominant male-fertility restoration alleles (Rf) and their recessive male-sterility maintenance counterparts (rf). Results A high density linkage map based on single nucleotide polymorphism (SNP) markers was generated using an F2 mapping population and genotyping-by-sequencing (GBS). The parents of this cross were ‘ICMA 02777’ and ‘ICMR 08888’, which segregate for the A4 Rf locus. The linkage map consists of 460 SNP markers distributed mostly evenly and has a total length of 462 cM. The segregation ratio of male-fertile and male-sterile plants (3:1) based on pollen production (presence/absence) indicated monogenic dominant inheritance of male-fertility restoration. Correspondingly, a major quantitative trait locus (QTL) for pollen production was found on linkage group 2, with cross-validation showing a very high QTL occurrence (97%). The major QTL was confirmed using selfed seed set as phenotypic trait, though with a lower precision. However, these QTL explained only 14.5% and 9.9% of the phenotypic variance of pollen production and selfed seed set, respectively, which was below expectation. Two functional KASP markers were developed for the identified locus. Conclusion This study identified a major QTL for male-fertility restoration using a GBS-based linkage map and developed KASP markers which support high-throughput screening of the haploblock. This is a first step toward marker-assisted selection of A4 male-fertility restoration and male-sterility maintenance in pearl millet. Electronic supplementary material The online version of this article (10.1186/s12870-018-1267-8) contains supplementary material, which is available to authorized users.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a staple crop for the people of arid and semi-arid regions of the world. It is fast gaining importance as a climate resilient nutricereal. Exploiting the bold seeded, semi-dwarf, and early flowering genotypes in pearl millet is a key breeding strategy to enhance yield, adaptability, and for adequate food in resource-poor zones. Genetic variation for agronomic traits of pearl millet inbreds can be used to dissect complex traits through quantitative trait locus (QTL) mapping. This study was undertaken to map a set of agronomically important traits like flowering time (FT), plant height (PH), panicle length (PL), and grain weight (self and open-pollinated seeds) in the recombinant inbred line (RIL) population of ICMB 841-P3 × 863B-P2 cross. Excluding grain weight (open pollinated), heritabilities for FT, PH, PL, grain weight (selfed) were in high to medium range. A total of six QTLs for FT were detected on five chromosomes, 13 QTLs for PH on six chromosomes, 11 QTLs for PL on five chromosomes, and 14 QTLs for 1,000-grain weight (TGW) spanning five chromosomes. One major QTL on LG3 was common for FT and PH. Three major QTLs for PL, one each on LG1, LG2, and LG6B were detected. The large effect QTL for TGW (self) on LG6B had a phenotypic variance (R2) of 62.1%. The R2 for FT, TGW (self), and PL ranged from 22.3 to 59.4%. A total of 21 digenic interactions were discovered for FT (R2 = 18–40%) and PL (R2 = 13–19%). The epistatic effects did not reveal any significant QTL × QTL × environment (QQE) interactions. The mapped QTLs for flowering time and other agronomic traits in present experiment can be used for marker-assisted selection (MAS) and genomic selection (GS) breeding programs.

Pearl millet is a crop of the semi-arid tropics having high degree of genetic diversity and variable tolerance to drought stress. To investigate drought tolerance mechanism that possibly accounts for differences in drought tolerance, four recombinant inbred lines from a high resolution cross (HRC) were selected for variability in their transpiration rate (Tr) response to vapour pressure deficit (VPD) conditions. The differential Tr response of the genotypes to increased VPD conditions was used to classify the genotypes as sensitive or insensitive to high VPD. Aquaporin (AQP) genes PgPIP1;1, PgPIP1;2 , PgPIP2;1 , PgPIP2;3 , PgPIP2;6 , PgTIP1;1 and PgTIP2;2 were cloned. Phylogenetic analysis revealed that the cloned PgAQPs were evolutionarily closer to maize AQPs than to rice. PgAQP genes, including PgPIP1;1 and PgPIP2;6 in root tissue showed a significant expression pattern with higher expression in VPD-insensitive genotypes than VPD-sensitive genotypes under low VPD conditions (1.2 kPa) i.e when there is no high evaporative demand from the atmosphere. PgAQP genes (PgPIP2;1 in leaf and root tissues; PgPIP1;2 and PgTIP2;2 in leaf and PgPIP2;6 in root) followed a diurnal rhythm in leaves and roots that have either higher or lower expression levels at different time intervals. Under high VPD conditions (4.21 kPa), PgPIP2;3 showed higher transcript abundance in VPD-insensitive genotypes, and PgPIP2;1 in VPD-sensitive genotypes, while rest of the PgAQPs showed differential expression. Our current hypothesis is that these differences in the expression of AQP genes under different VPDs suggests a role of the AQPs in tuning the water transport pathways with variation between genotypes.

Pearl millet [Pennisetum glaucum (L.) R. Br] is a food security crop for millions living in drylands of Africa and Asia. Its production on acid sandy soils of the Sahel is limited by erratic rainfall and poor soil fertility, especially low P soils. We sought to elucidate the genetic variation in West and Central African landrace-derived inbred lines for grain yield under low P conditions, to determine their performance as inbred lines per se and in hybrid combinations, and to determine quantitative-genetic parameters to derive an appropriate breeding strategy to enhance grain yield under low P conditions. We evaluated a total of 155 landrace-derived inbred lines as well as their testcrosses in four locations during two years under two treatments, high P (HP; with P fertilization) and low P (LP; without P fertilization). Results revealed significant effects for genotypes, P-level, genotype × P-level, as well as genotype × environment interactions. Grain yield reductions under LP treatment ranged from 7.9 to 35.5%, and 11.2 to 60.9% for inbred lines and testcrosses respectively, with positive midparent heterosis averaging 43.5% under LP. We conclude that direct selection of testcrosses under LP is more effective and that indirect selection for testross performance from inbred line performance is not desirable.

Pearl millet (Cenchrus americanus (L.) Morrone) is one of the most important cereals in West and Central Africa (WCA). Human populations in WCA are strongly affected by micronutrient deficiencies. Biofortification, the development of pearl millet varieties with enhanced micronutrient levels is recognized as a suitable approach to reduce this widespread health problem. To assess the potential of biofortification of WCA pearl millet germplasm, we studied quantitative-genetic parameters of eight mineral densities in whole and decorticated grains, their stability over environments and the correlations among minerals and agro morphological traits. The study included 72 WCA pearl millet genotypes which were grown in three environments in Niger, contrasting in soil fertilization. Significant genotypic effects, moderate estimates of heritability, and genetic variation for mineral densities, especially for Fe and Zn, indicate a high potential for biofortification of WCA pearl millet. However, screening of additional landraces or introgression of favorable alleles from highly nutrient dense Indian germplasm could expedite achievement of higher densities. Genotype-by environment interaction effects were significant for Fe and Zn grain densities, showing the importance of multi-environmental evaluation to identify stable genotypes. Identified genotypes with relatively stable Fe and Zn grain densities appear suitable for use in future WCA pearl millet biofortification breeding programs.

Striga hermonthica (Del.) Benth. is a persistent threat to pearl millet [Cenchrus americanus (L.) Morrone, comb. nov.] production, especially in West Africa. This study aimed at evaluating the response of a diversified pearl millet genepool to five cycles of recurrent selection targeting Striga resistance and panicle yield, and to a lesser extent downy mildew [Sclerospora graminicola (Sacc.) J. Schroet.] resistance. Two-hundred full-sib families (FS) representing the C5 selection cycle were evaluated together with the genepool parental landraces, experimental varieties derived from previous cycles and local checks in Striga-infested fields at Sadoré (Niger) and Cinzana (Mali). Substantial and mostly significant selection progress could be documented. The accumulated percentage gain from selection amounted to 51%/1% lower Striga infestation (measured by area under Striga number progress curve, ASNPC), 46%/62% lower downy mildew incidence, and 49%/31% higher panicle yield of the C5-FS compared to the mean of the genepool parents at Sadoré/Cinzana, respectively. Experimental varieties selected from previous cycles also revealed lower ASNPC and mostly higher yield compared to genepool parents at their selection sites. Significant genetic variation among the C5-FS and operative heritabilities of 76% (Cinzana), 84% (Sadoré) and 34% (combined across locations) for ASNPC will enable continued selection gain for Striga resistance. High genotype×environment interaction variances for all target traits suggest that different experimental varieties need to be extracted from the genepool for different sites. The genepool-derived varieties will be further validated on-farm and are expected to contribute to integrated Striga control in pearl millet in West Africa.

The control of reactive oxygen species (ROS) and the stability of photosynthetic pigments under stress conditions are hypothesized to contribute to drought tolerance. Here we studied how ascorbic peroxidase (APX), superoxide dismutase (SOD), catalase (CAT) isozyme activities and chlorophyll a, b (Chl a, b) and carotenoids (Car) contents responded to water stress and whether they related to presence of a terminal drought tolerance QTL in pearl millet. We used PRLT2/89-33 (QTL donor), H77/833-2 (sensitive), and near-isogenic lines (QTL-NILs) introgressed with the QTL in H77/833-2 background. Under water stress there was no significant change in the total APX activity; only the proportional APX5 activity increased, with higher band intensity in tolerant genotypes. There were no significant changes in total activities of CAT and SOD under water stress, with similar band intensities in all genotypes, and a new CAT isozyme was induced in all genotypes. The photosynthetic pigment content decreased under water stress, although not differently in any genotype. Under water stress, the activities of most APX, CAT and SOD isozymes were closely related to the total chlorophyll/carotenoids ratio. Overall, besides APX5, water stress did not lead to major changes in the profile of isoenzymes involved in ROS scavenging. Similarly, the pigment content under stress did not discriminate genotypes according to the presence/absence of the QTL. This absence of discrimination for the ROS scavenging enzymes and for the pigment content under stress suggests that these traits may not play a key role in terminal drought tolerance in pearl millet.

A set of 22 pearl millet inbred lines including the parents of eleven mapping populations, was screened with 627 markers including 100 pearl millet genomic SSRs (gSSRs), 60 pearl millet EST-SSRs (eSSRs), 410 intron sequence haplotypes (ISHs), and 57 exon sequence haplotypes (ESHs). In all, 267 (59%) of the markers were informative for at least one of the 11 mapping populations, which segregate for traits like drought and salinity tolerance; host plant resistance to downy mildew, rust and blast; fertility restoration and sterility and maintenance of cytoplasmic male sterility etc. An average of 116 polymorphic markers was identified per mapping population. The average PIC values and number of profiles (P) per polymorphic marker were: gSSRs (PIC = 0.62, P = 6.1), ISHs (PIC = 0.39, P = 2.6), eSSRs (PIC = 0.36, P = 3.1) and ESHs (PIC = 0.35, P = 3.1). A high correlation (r > 0.97, P

Contact: fax: +91 40 30713074/30713075. E-mail address: r.k.varshney@cgiar.org; International audience; The transcription factor, DREB2A, is one of the promising candidate genes involved in dehydration tolerance in crop plants. In order to isolate DREB2A homologues across cereals (rice, barley and sorghum) and legumes (common bean and chickpea), specific or degenerate primers were used. Gene/phylogenetic trees were constructed using a non-redundant set of 19 DREB1A and 27 DREB2A amino acid sequences and were combined with taxonomic/species tree to prepare reconciled phylogenetic trees. In total, 86 degenerate primers were designed for different clades and 295 degenerate primer combinations were used to amplify DREB homologues in targeted crop species. Successful amplification of DREB2A was obtained in case of sorghum. In parallel, gene-specific primers were used to amplify DREB2A homologues in rice, barley, common bean and chickpea. Seven to eight diverse genotypes from targeted species were used for sequence analysis at DREB2A locus identified/isolated. A maximum of eight SNPs were found in the common bean DREB2A, indicating two distinct haplotypes, three SNPs with five haplotypes were observed in barley whereas a single SNP was observed in rice, sorghum and chickpea. Parsimony based phylogenetic tree revealed distinct clustering of cereals and legumes. Furthermore, alignment of corresponding amino acid sequences showed conservation of AP2 domain across the targeted species.

Pearl millet, a key staple crop of the semi-arid tropics, is mostly grown in water-limited conditions, and improving its performance depends on how genotypes manage limited water resources. This study investigates whether the control of water loss under non-limiting water conditions is involved in the terminal drought tolerance of pearl millet. Two pairs of tolerant x sensitive pearl millet genotypes, PRLT 2/89-33-H77/833-2 and 863B-P2-ICMB 841-P3, and near-isogenic lines (NILs), introgressed with a terminal drought tolerance quantitative trait locus (QTL) from the donor parent PRLT 2/89-33 into H77/833-2 (NILs-QTL), were tested. Upon exposure to water deficit, transpiration began to decline at lower fractions of transpirable soil water (FTSW) in tolerant than in sensitive genotypes, and NILs-QTL followed the pattern of the tolerant parents. The transpiration rate (Tr, in g water loss cm(-2) d(-1)) under well-watered conditions was lower in tolerant than in sensitive parental genotypes, and the Tr of NILs-QTL followed the pattern of the tolerant parents. In addition, Tr measured in detached leaves (g water loss cm(-2) h(-1)) from field-grown plants of the parental lines showed lower Tr values in tolerant parents. Defoliation led to an increase in Tr that was higher in sensitive than in tolerant genotypes. The differences in Tr between genotypes was not related to the stomatal density. These results demonstrate that constitutive traits controlling leaf water loss under well-watered conditions correlate with the terminal drought tolerance of pearl millet. Such traits may lead to more water being available for grain filling under terminal drought.

The natural ability of plants to release chemical substances from their roots that have a suppressing effect on nitrifier activity and soil nitrification, is termed ‘biological nitrification inhibition’ (BNI). Though nitrification is one of the critical processes in the nitrogen cycle, unrestricted and rapid nitrification in agricultural systems can result in major losses of nitrogen from the plant-soil system. This nitrogen loss is due to the leaching of nitrate out of the rooting zone and emission of gaseous oxides of nitrogen to the atmosphere, where it causes serious pollution problems. Using a newly developed assay system that quantifies the inhibitory activity of plant roots (i.e. BNI capacity), it has been shown that BNI capacity is widespread among crops and pastures. A tropical pasture grass, Brachiaria humidicola has been used as a model system to characterize BNI function, where it was shown that BNIs can provide sufficient inhibitory activity to suppress soil nitrification and nitrous oxide emissions. Given the wide-range of genetic diversity found among the Triticeae, and the current availability of genetic tools for moving traits/genes across members, there is great potential for introducing/improving the BNI capacity of economically important members of the Triticeae (i.e. wheat, barley and rye). This review outlines the current status of knowledge regarding the potential for genetic improvement in the BNI capacity of the Triticeae. Such approaches are critical to the development of the next-generation of crops and production systems where nitrification is biologically suppressed/regulated to reduce nitrogen leakage and protect the environment from nitrogen pollution.

Crop tolerance to salinity is of high importance due to the extent and the constant increase in salt-affected areas in arid and semi-arid regions. Pearl millet (Pennistum glaucum), generally considered as fairly tolerant to salinity, could be an alternative crop option for salt affected areas. To explore the genotypic variability of vegetative-stage salinity tolerance, 100 pearl millet lines from ICRISAT breeding programs were first screened in a pot culture containing Alfisol with 250 mM NaCl solution as basal application. Subsequently, 31 lines including many parents of commercial hybrids, selected from the first trial were re-tested for confirmation of the initial salinity responses. Substantial variation for salinity tolerance was found on the basis of shoot biomass ratio (shoot biomass under salinity/ non-saline control) and 22 lines with a wide range of tolerance varying from highly tolerant to sensitive entries were identified. The performance of the genotypes was largely consistent across experiments. In a separate seed germination and seedling growth study, the seed germination was found to be adversely affected (more than 70% decrease) in more than half of the genotypes with 250 mM concentration of NaCl. The root growth ratio (root growth under salinity/control) as well as shoot growth ratio was measured at 6 DAS and this did not reflect the whole plant performance at 39 DAS. In general, the whole plant salinity tolerance was associated with reduced shoot N content, increased K+ and Na+ contents. The K+/Na+ and Ca++/Na+ ratios were also positively related to the tolerance but not as closely as the Na+ content. Therefore, it is concluded that a large scope exists for improving salt tolerance in pearl millet and that shoot Na+ concentration could be considered as a potential non-destructive selection criterion for vegetative-stage screening. The usefulness of this criterion for salinity response with respect to grain and stover yield remains to be investigated.

Genetic improvement of salt tolerance is of high importance due to the extent and the constant increase in salt affected areas. Sorghum [Sorghum bicolor (L.) Moench] has been considered relatively more salt tolerant than maize and has the potential as a grain and fodder crop for salt affected areas. One hundred sorghum genotypes were screened for salinity tolerance in pots containing Alfisol and initially irrigated with a 250-mM NaCl solution in a randomized block design with three replications. Subsequently 46 selected genotypes were assessed in a second trial to confirm their responses to salinity. Substantial variation in shoot biomass ratio was identified among the genotypes. The performance of genotypes was consistent across experiments. Seven salinity tolerant and ten salinity sensitive genotypes are reported. Relative shoot lengths of seedlings were genetically correlated to the shoot biomass ratios at all stages of sampling though the relationships were not close enough to use the trait as a selection criterion. In general, the whole-plant tolerance to salinity resulted in reduced shoot Na+ concentration. The K+/Na+ and Ca2+/Na+ ratios were also positively related to tolerance but with a lesser r2. Therefore, it is concluded that genotypic diversity exists for salt tolerance biomass production and that Na+ exclusion from the shoot may be a major mechanism involved in that tolerance.

Genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation., Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.

Highlight We present a new concept combining novel 3D scanning of the plant canopy with seamless assessment of plant water use to measure plant traits influencing the water budget., In this paper, we describe the thought process and initial data behind the development of an imaging platform (LeasyScan) combined with lysimetric capacity, to assess canopy traits affecting water use (leaf area, leaf area index, transpiration). LeasyScan is based on a novel 3D scanning technique to capture leaf area development continuously, a scanner-to-plant concept to increase imaging throughput and analytical scales to combine gravimetric transpiration measurements. The paper presents how the technology functions, how data are visualised via a web-based interface and how data extraction and analysis is interfaced through ‘R’ libraries. Close agreement between scanned and observed leaf area data of individual plants in different crops was found (R2 between 0.86 and 0.94). Similar agreement was found when comparing scanned and observed area of plants cultivated at densities reflecting field conditions (R2 between 0.80 and 0.96). An example in monitoring plant transpiration by the analytical scales is presented. The last section illustrates some of the early ongoing applications of the platform to target key phenotypes: (i) the comparison of the leaf area development pattern of fine mapping recombinants of pearl millet; (ii) the leaf area development pattern of pearl millet breeding material targeted to different agro-ecological zones; (iii) the assessment of the transpiration response to high VPD in sorghum and pearl millet. This new platform has the potential to phenotype for traits controlling plant water use at a high rate and precision, of critical importance for drought adaptation, and creates an opportunity to harness their genetics for the breeding of improved varieties.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is the staple cereal of the hottest, driest areas of the tropics and subtropics. Drought stress is a regular occurrence in these regions, making stress tolerance an essential attribute of new pearl millet cultivars. Recent breeding research has mapped several quantitative trait loci (QTLs) for components of grain and stover yield per se, as well as yield maintenance, under terminal drought stress conditions. We report here the evaluation of these QTLs as possible selection criteria for improving stress tolerance of an elite hybrid cultivar. Initial evaluations, based on hybrids made with topcross pollinators bred from lines selected directly from the mapping population, indicated an advantage to the QTL-based topcross hybrids. This advantage seemed to be related to a particular plant phenotype that was similar to that of the drought tolerant parent of the mapping population. Subsequent evaluations were based on testcross hybrids of drought tolerance QTL introgression lines in the background of the drought-sensitive parent of the mapping population, H 77/833-2. These introgression lines were bred by limited marker-assisted backcrossing of a putative major drought tolerance QTL into H 77/833-2 from the mapping population's drought tolerant parent. Several of these QTL introgression lines had a significant positive general combining ability for grain yield under terminal stress and significantly out-yielded testcross hybrids made with the original recurrent parent both in unrelieved terminal drought stress and in gradient stress evaluations.

Grain micronutrient content assessment is important in breeding pearl millet, in order to maintain or improve its high nutritional quality. Grain samples of 12 farmer-preferred pearl millet varieties produced in four representative environments in Niger during the 2013 rainy season were assessed for Fe, Zn, Al and P grain densities using energy dispersive X-ray fluorescence spectroscopy. Combined analysis of variance revealed significant (P < 0.01) variation among entries across environments only for Fe grain density, which had a broad-sense heritability of 89%. Fe grain density varied from 30.4 to 39.2 mg kg -1 among these varieties, with a mean of 32.4 mg kg -1 . Among the 12 varieties, ICRI-Tabi and ICMV-IS 13131 (reselected ICRI-Tabi) showed the highest Fe grain densities. © 2016 International Formulae Group. All rights reserved. Keywords: Genetic variability, Grain iron, heritability, malnutrition, micronutrients, pearl millet

Barnyard millet (Echinochloa spp.) is an important crop for many smallholder farmers in southern and eastern Asia. It is valued for its drought tolerance, rapid maturation, and superior nutritional qualities. Despite these characteristics there are almost no genetic or genomic resources for this crop in either cultivated species [E. colona (L.) Link and E. crus-galli (L.) P. Beauv.]. Recently, a core collection of 89 barnyard millet accessions was developed at the genebank at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). To enhance the use of this germplasm and genomic research in barnyard millet improvement, we report the genetic characterization of this core collection using whole-genome genotyping-by-sequencing. We identified several thousand single-nucleotide polymorphisms segregating in the core collection, and we use them to show patterns of population structure and phylogenetic relationships among the accessions. We determine that there are probably four population clusters within the E. colona accessions and three such clusters within E. crus-galli. These clusters match phylogenetic relationships but by and large do not correspond to classification into individual races or clusters based on morphology. Geospatial data available for a subset of samples indicates that the clusters probably originate from geographic divisions. In all, these data will be useful to breeders working to improve this crop for smallholder farmers. This work also serves as a case study of how modern genomics can rapidly characterize crops, including ones with little to no prior genetic data.

Pearl millet (Pennisetum glaucum) varieties grown in semiarid Africa and Asia have low grain yields. Information on heterosis and combining ability of diverse open-pollinated cultivars, breeding populations, and genepools is needed for efficient choice of breeding methods and parental materials to use in developing productive base populations for this crop. Data for grain and biomass yield, growth rate, time to flowering, plant height, panicle length, and productive tillers were collected from an 11-parent variety cross diallel of diverse pearl millet populations evaluated in five field environments (rainy season of 1993 in Patancheru, Andhra Pradesh and Bhavanisagar, Tamil Nadu; dry summer season of 1994 and rainy seasons of 1994 and 1995 in Patancheru) in peninsular India. Data were summarized using the Gardner-Eberhart Analysis II. When genotype x environment interactions were significant, ranks of parental general combining abilities (GCA) were used to identify particular environments and parents contributing most to these interactions. Parental population effects were significant for all characters, as were differences in GCA. Populations NWC C2, AfPop 88, and LHGP consistently had the poorest ranks for general combining ability for grain yield across test environments. Populations ICMV 91059, SenPop, ICMP 91751, and ICMP 92951 constitute a genetically diverse subset of the parents that consistently had the best ranks for grain yield GCA across test environments. With ICMV 155 (crosses of which performed poorly in only one of five test environments), this latter group is a good source of more broad-based breeding populations for dual-purpose pearl millet improvement targeting peninsular India.

This chapter focuses on the usage of stay-green as a breeding target under water-limited conditions. It reviews recent progress in different areas of stay-green research, with a particular focus on sorghum, where this trait has been most studied. Given the potential benefit of stay-green, genotypes displaying this trait have been used to identify the genomic regions responsible for this phenotype. Several quantitative trait loci (QTLs) have been identified, using different breeding populations and stay-green QTL donors, and different types of drought stress. The chapter reviews the experimental conditions in which phenotyping for stay-green has taken place and the different ways of assessing this phenotype, either from leaf senescence curves or leaf greenness assessments. It summarizes current work being done at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), in Andhra Pradesh, India to introgress several known QTLs for staygreen into various agronomically elite genetic backgrounds.

Variations in plant pathogenic fungi arise largely through sexual processes, heterozygosity and somatic recombination, mutation, and selection. Large shifts in pathogenicity occur due to changes in host cultivar and environment. The amount of genetic variation in the pathogen population influences its ability to adapt to fluctuating environmental conditions and the changing host cultivars. In general, highly variable populations are better adapted than those with little variation. Pathogenicity or virulence has been used as the genetic marker in all studies where variability has been assessed through virulence surveys, using host differentials containing different resistance genes.

Traits influencing plant water use eventually define the fitness of genotypes for specific rainfall environments. We assessed the response of several water use traits to vapour pressure deficit (VPD) in pearl millet (Pennisetum glaucum (L.) R.Br.) genotypes known to differ in drought adaptation mechanisms: PRLT 2/89–33 (terminal drought-adapted parent), H 77/833–2 (terminal drought-sensitive parent) and four near-isogenic lines introgressed with a terminal drought tolerance quantitative trait locus (QTL) from PRLT 2/89–33 (ICMR01029, ICMR01031, ICMR02042, and ICMR02044). Plant water use traits at various levels of plant organisation were evaluated in seven experiments in plants exposed either transiently or over the long term to different VPD regimes: biomass components, transpiration (water usage per time unit) and transpiration rate (TR) upon transient VPD increase (g H2O cm–2 h–1)), transpiration efficiency (g dry biomass per kg H2O transpired), leaf expansion rate (cm per thermal time unit) and root anatomy (endodermis dimensions)). High VPD decreased biomass accumulation by reducing tillering, the leaf expansion rate and the duration of leaf expansion; decreased root endodermis cell size; and increased TR and the rate of TR increase upon gradual short-term VPD increases. Such changes may allow plants to increase their water transport capacity in a high VPD environment and are genotype-specific. Some variation in water use components was associated with terminal drought adaptation QTL. Knowledge of water use traits’ plasticity in growth environments that varied in evaporative demand, and on their genetic determinacy, is necessary to develop trait-based breeding approaches to complex constraints.

Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9 Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb). The relative abundance, density, composition and putative annotations of di-, tri-, tetra- and penta-nucleotide repeats have been compared and SSR containing ESTs (SSR-ESTs) have been clustered to give a non-redundant set of EST-SSRs, available in a database. Further, a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible, stay-green drought tolerant mapping population parent 'E 36-1' and its Striga-resistant, non-stay-green counterpart 'N13'. Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines. Over half of these markers have been genotyped on 94 RILs from the (N13 x E 36-1)-based mapping population, with 42 markers mapping onto the ten sorghum linkage groups. This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding. The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database (http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html).

The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineense accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discussed.