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, 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 tolerantxsensitive 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.
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.
Pearl millet
(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 (
) of 62.1%. The
for FT, TGW (self), and PL ranged from 22.3 to 59.4%. A total of 21 digenic interactions were discovered for FT (
= 18-40%) and PL (
= 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.
Low transpiration rates in pearl millet under fully irrigated conditions decrease plant water use at vegetative stage and then increase the water availability during grain filling and finally the ...terminal drought tolerance. Hundred and thirteen recombinant inbred lines developed from a cross between H77/833-2 and PRLT2/89-33 (terminal drought-sensitive × tolerant genotype) were evaluated to map transpiration rate (Tr, a proxy for canopy conductance), organ weights, leaf area and thickness and to study their interactions. Transpiration rate was increased by two H77/833-2 and two PRLT2/89-33 alleles on linkage group (LG) 2, whose importance depended on the vapor pressure deficit. The two H77/833-2 and one PRLT2/89-33 alleles co-mapped to a previously identified major terminal drought tolerance quantitative trait locus (QTL), although in a much smaller genetic interval. The other Tr allele from H77/833-2 also enhanced biomass dry weight and co-located with a formerly identified stover and tillering QTL. Leaf characteristics were linked to two loci on LG7. Plant water use was increased and decreased by different loci combinations for Tr, tillering and leaf characteristics, whose respective importance depended on the environmental conditions. Therefore, different alleles influence plant water use and have close interactions with one another and with the environment, so that different ideotypes for plant water use exist or could be designed from specific allele combinations conferring particular physiological characteristics for specific adaptation to a range of terminal drought conditions.
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.
Migrating grazers and carnivores respond to seasonal changes in the environment and often match peaks in resource abundance. However, it is unclear whether and how frugivorous animals use ...phenological events to time migration, especially in the tropics.
The straw‐coloured fruit bat Eidolon helvum, Africa's most gregarious fruit bat, forms large seasonal colonies throughout much of sub‐Saharan Africa. We hypothesized that aggregations of E. helvum match the timing of their migration with phenologies of plant growth or precipitation.
Using monthly colony counts from across much of the species' range, we matched peak colony size to landscape phenologies and explored the variation among colonies matching the overall closest phenological event.
Peak colony size was closest to the peak instantaneous rate of green‐up, and sites with closer temporal matching were associated with higher maximum greenness, short growing season and larger peak colony size. Eidolon helvum seem to time their migrations to move into highly seasonal landscapes to exploit short‐lived explosions of food and may benefit from collective sensing to time migrations.
The link between rapid changes in colony size and phenological match may also imply potential collective sensing of the environment. Overall decreasing bat numbers along with various threats might cause this property of large colonies to be lost.
Remote sensing data, although, indirectly linked to fruiting events, can potentially be used to globally describe and predict the migration of frugivorous species in a changing world.
Read the free Plain Language Summary for this article on the Journal blog.
Read the free Plain Language Summary for this article on the Journal blog.
BACKGROUNDPearl 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).RESULTSA 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.CONCLUSIONThis 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.
•Identified pearl millet genotypes showing contrasting transpiration response to high vapor pressure deficit (VPD).•Cloned seven PgAQP genes using homology based gene identification.•PgAQP proteins ...were found to be evolutionarily closer to maize than rice.•PgAQPs were induced in VPD-insensitive genotypes under low and high VPD conditions.•PgPIP2;1, PgPIP1;2, PgTIP2;2 and PgPIP2;6 genes followed a diurnal rhythm of expression.
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 (1.2kPa) 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 (4.21kPa), 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.
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-RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F
was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F
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-Single Nucleotide Polymorphism (GBS-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 (
), NBS-LRR protein (
), ankyrin-repeat protein (
), senescence-associated protein (
), WD40 (
), CPK1 adapter protein (
), LEA2 protein (
) and an expressed protein (
). 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)-PCR.
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