Evolutionary maintenance of dioecy is a complex phenomenon and varies by species and underlying pathways. Also, different sexes may exhibit variable resource allocation (RA) patterns among the ...vegetative and reproductive functions. Such differences are reflected in the extent of sexual dimorphism. Though rarely pursued, investigation on plant species harbouring intermediate sexual phenotypes may reveal useful information on the strategy pertaining to sex-ratios and evolutionary pathways. We studied H. rhamnoides ssp. turkestanica, a subdioecious species with polygamomonoecious (PGM) plants, in western Himalaya. The species naturally inhabits a wide range of habitats ranging from river deltas to hill slopes. These attributes of the species are conducive to test the influence of abiotic factors on sexual dimorphism, and RA strategy among different sexes. The study demonstrates sexual dimorphism in vegetative and reproductive traits. The sexual dimorphism index, aligned the traits like height, number of branches, flower production, and dry-weight of flowers with males while others including fresh-weight of leaves, number of thorns, fruit production were significantly associated with females. The difference in RA pattern is more pronounced in reproductive traits of the male and female plants, while in the PGM plants the traits overlap. In general, habitat conditions did not influence either the extent of sexual dimorphism or RA pattern. However, it seems to influence secondary sex-ratio as females show their significant association with soil moisture. Our findings on sexual dimorphism and RA pattern supports attributes of wind-pollination in the species. The observed extent of sexual dimorphism in the species reiterates limited genomic differences among the sexes and the ongoing evolution of dioecy via monoecy in the species. The dynamics of RA in the species appears to be independent of resource availability in the habitats as the species grows in a resource-limited and extreme environment.
Summary
Root‐knot nematodes (RKNs, Meloidogyne incognita) are economically important endoparasites with a wide host range. We used a comprehensive transcriptomic approach to investigate the ...expression of both tomato and RKN genes in tomato roots at five infection time intervals from susceptible plants and two infection time intervals from resistant plants, grown under soil conditions. Differentially expressed genes during susceptible (1827, tomato; 462, RKN) and resistance (25, tomato; 160, RKN) interactions were identified. In susceptible responses, tomato genes involved in cell wall structure, development, primary and secondary metabolite, and defence signalling pathways, together with RKN genes involved in host parasitism, development and defence, are discussed. In resistance responses, tomato genes involved in secondary metabolite and hormone‐mediated defence responses, together with RKN genes involved in starvation stress‐induced apoptosis, are discussed. In addition, 40 novel differentially expressed RKN genes encoding secretory proteins were identified. Our findings provide novel insights into the temporal regulation of genes involved in various biological processes from tomato and RKN simultaneously during susceptible and resistance responses, and reveal the involvement of a complex network of biosynthetic pathways during disease development.
Drought stress leads to a significant amount of agricultural crop loss. Thus, with changing climatic conditions, it is important to develop resilience measures in agricultural systems against drought ...stress. Roots play a crucial role in regulating plant development under drought stress. In this review, we have summarized the studies on the role of roots and root‐mediated plant responses. We have also discussed the importance of root system architecture (RSA) and the various structural and anatomical changes that it undergoes to increase survival and productivity under drought. Various genes, transcription factors, and quantitative trait loci involved in regulating root growth and development are also discussed. A summarization of various instruments and software that can be used for high‐throughput phenotyping in the field is also provided in this review. More comprehensive studies are required to help build a detailed understanding of RSA and associated traits for breeding drought‐resilient cultivars.
Core Ideas
The root is the first plant organ to sense drought and responds through morphological, anatomical, and genetic changes.
These changes explore and secure resources with minimal metabolic cost.
Using high‐throughput and advanced phenotyping, root system architecture (RSA) can be studied comprehensively.
Such a study can pave the way for strategic modifications in RSA to develop resilient crops.
L. (safflower) is an important oilseed crop producing seed oil rich in unsaturated fatty acids. Scarcity of identified marker-trait associations is a major limitation toward development of successful ...marker-assisted breeding programs in safflower. In the present study, a safflower panel (CartAP) comprising 124 accessions derived from two core collections was assayed for its suitability for association mapping. Genotyping of CartAP using microsatellite markers revealed significant genetic diversity indicated by Shannon information index (
= 0.7537) and Nei's expected heterozygosity (
= 0.4432). In Principal Coordinate Analysis, the CartAP accessions were distributed homogeneously in all quadrants indicating their diverse nature. Distance-based Neighbor Joining analysis did not delineate the CartAP accessions in consonance with their geographical origin. Bayesian analysis of population structure of CartAP demonstrated the unstructured nature of the association panel. Kinship analysis at population (
) and individual level (
) revealed absence of or weak relatedness between the CartAP accessions. The above parameters established the suitability of CartAP for association mapping. We performed association mapping using phenotypic data for eight traits of agronomic value (
., seed oil content, oleic acid, linoleic acid, plant height, number of primary branches, number of capitula per plant, 100-seed weight and days to 50% flowering) available for two growing seasons (2011-2012 and 2012-2013) through General Linear Model and Mixed Linear Model. Our study identified ninety-six significant marker-trait associations (MTAs;
< 0.05) of which, several MTAs with correlation coefficient (
) > 10% were consistently represented in both models and in both seasons for traits
., oil content, oleic acid content, linoleic acid content and number of primary branches. Several MTAs with high
-values were detected either in a majority or in some environments (models and/or seasons). Many MTAs were also common between traits (
., oleic/linoleic acid content; plant height/days to 50% flowering; number of primary branches/number of capitula per plant) that showed positive or negative correlation in their phenotypic values. The marker-trait associations identified in this study will facilitate marker-assisted breeding and identification of genetic determinants of trait variability.
Infraspecific floral trait variations may appear in response to elevational differences in alpine plant species. There is enormous information on the selection of such morphs mediated by biotic ...and/or abiotic variables. Whether such differences contribute to differences in reproductive strategy and mating outcomes is rarely investigated. We investigated these aspects in two distinct elevational floral morphs (Red and Pink) of
Sm. in Western Himalaya. The red morphs occupy the lower elevations while pink morphs the higher elevations. The two morphs differ in floral traits like phenology, dimension, display, quality of floral rewards, and pollinators that happen to influence interaction with available pollinator pool at each elevation. The pink morph exhibits entomophily, while the red ones show ornithophily. Although experimental pollinations established that both the morphs are self-compatible, selfing results in significantly lower fruit-set than either cross- or open-pollinations. The outcrossing rate in the red morph, as determined by using simple sequence repeat (SSR) markers, was higher (t
=0.82) than that in the pink morph (t
=0.76), with a tendency of the latter to be shifting towards mixed-mating strategy. However, the extent of biparental inbreeding was comparable among the two morphs. It is inferred that the differences in the mating outcomes among the morphs in the tree species are linked to those emerging from floral traits and the pollination by different functional groups of floral visitors.
Root-knot nematodes (RKNs, Meloidogyne spp.) are the most damaging plant parasites causing severe losses to crop production. The present study reports genome-wide identification and characterization ...of both tomato and RKN miRNAs simultaneously from RKN-infected susceptible tomato roots using high-throughput sequencing technique. RNAseq data from 11 small RNA libraries derived from 5 disease development stages identified 281 novel miRNAs of tomato in addition to 52 conserved and 4 variants of conserved miRNAs. Additionally, the same set of RNAseq data identified 38 conserved and 290 novel RKN miRNAs. Both tomato and RKN miRNAs showed differential expression at 5 stages of disease development based on digital expression profiles. In tomato, further validation through qRT-PCR confirmed that majority of miRNAs were significantly upregulated during susceptible response whereas downregulated during resistance response. The predicted targets of 8 conserved and 1 novel miRNAs were validated through 5'RLM-RACE. A negative correlation between expression profiles of a few conserved miRNAs (miR156, miR159, miR164 and miR396) and their targets (SBP, GAMYB-like, NAC and GRF1 transcription factor) was confirmed. A novel Sly_miRNA996 also showed a negative correlation with its target MYB-like transcription factor. These results indicate that the conserved and novel tomato miRNAs are involved in regulating developmental changes in host root during RKN infection. In RKN, the targets of conserved miRNAs were also predicted and a few of their predicted target genes are known to be involved in nematode parasitism. Further, the potential roles of both tomato and RKN miRNAs have been discussed.
Safflower (
Carthamus tinctorius
L.), an oilseed crop, is severely affected by
Fusarium oxysporum
f. sp.
carthami
(Foc), a fungus causing Fusarium wilt (FW) resulting in up to 80% yield loss. In the ...present study, we used a panel of 84 diverse accessions from the composite core collection to perform association mapping for FW-resistance. Hydroponics-based screening resulted in categorization of 84 accessions as 31 immune, 19 highly resistant, 9 moderately resistant, 4 moderately susceptible, and 21 highly susceptible. Genotyping with a combination of 155 AFLP and 144 SSR markers revealed substantial genetic differentiation and structure analysis identified three main subpopulations (
K
= 3) with nearly 35% of admixtures in the panel. Kinship analysis at individual and population level revealed absence of or weak relatedness between the accessions. Association mapping with General Linear Model and Mixed Linear Model identified 4 marker-trait associations (MTAs) significantly linked with the FW-resistance trait. Of these, 3 robust MTAs identified in both the models exhibited phenotypic variance ranging from 4.09 to 6.45%. Locus-128 showing a low
P-
value and high phenotypic variance was identified as a promising marker-trait association that will facilitate marker-assisted breeding for FW-resistance in safflower.
Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for ...improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing.
Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to cultivated safflower and formed a distinct cluster. The cluster analysis also distinguished diploid and tetraploid wild species of safflower.
Next generation sequencing of safflower genome generated a large set of microsatellite markers. The novel markers developed in this study will add to the existing repertoire of markers and can be used for diversity analysis, synteny studies, construction of linkage maps and marker-assisted selection.
, commonly known as water lily, is the largest and most widely distributed genus in the order Nymphaeales. The importance of
in wetland ecosystems and their increased vulnerability make them a great ...choice for conservation and management. In this work, we studied genetic diversity in a collection of 90
and 92
individuals from six different states of India, i.e., Assam, Manipur, Meghalaya, Maharashtra, Goa, and Kerala, using simple sequence repeat (SSR) markers developed by low throughput Illumina sequencing (10X coverage of genome) of
.
is native to India, whereas
is suggested to be introduced to the country for its aesthetic and cultural values. The study revealed extensive polymorphism in
, while in
, no apparent genetic divergence was detected prompting us to investigate the reason(s) by studying the reproductive biology of the two species. The study revealed that
predominantly reproduces asexually which has impacted the genetic diversity of the species to a great extent. This observation is of immense importance for a successful re-establishment of
species during restoration programs of wetlands. The information generated on reproductive behaviors and their association with genotypic richness can help in strategizing genetic resource conservation, especially for species with limited distribution. The study has also generated 22,268 non-redundant microsatellite loci, out of which, 143 microsatellites were tested for polymorphism and polymorphic markers were tested for transferability in five other
species, providing genomic resources for further studies on this important genus.
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