Proline has been recognized as a multi-functional molecule, accumulating in high concentrations in response to a variety of abiotic stresses. It is able to protect cells from damage by acting as both an osmotic agent and a radical scavenger. Proline accumulated during a stress episode is degraded to provide a supply of energy to drive growth once the stress is relieved. Proline homeostasis is important for actively dividing cells as it helps to maintain sustainable growth under long-term stress. It also underpins the importance of the expansion of the proline sink during the transition from vegetative to reproductive growth and the initiation of seed development. Its role in the reproductive tissue is to stabilize seed set and productivity. Thus, to cope with abiotic stress, it is important to develop strategies to increase the proline sink in the reproductive tissue. We give a holistic account of proline homeostasis, taking into account the regulation of proline synthesis, its catabolism, and intra-and intercellular transport, all of which are vital components of growth and development in plants challenged by stress.

A set of 2486 single nucleotide polymorphisms (SNPs) were compiled in chickpea using four approaches, namely (i) Solexa/Illumina sequencing (1409), (ii) amplicon sequencing of tentative orthologous genes (TOGs) (604), (iii) mining of expressed sequence tags (ESTs) (286) and (iv) sequencing of candidate genes (187). Conversion of these SNPs to the cost-effective and flexible throughput Competitive Allele Specific PCR (KASPar) assays generated successful assays for 2005 SNPs. These marker assays have been designated as Chickpea KASPar Assay Markers (CKAMs). Screening of 70 genotypes including 58 diverse chickpea accessions and 12 BC3F2 lines showed 1341 CKAMs as being polymorphic. Genetic analysis of these data clustered chickpea accessions based on geographical origin. Genotyping data generated for 671 CKAMs on the reference mapping population (Cicer arietinum ICC 4958 × Cicer reticulatum PI 489777) were compiled with 317 unpublished TOG-SNPs and 396 published markers for developing the genetic map. As a result, a second-generation genetic map comprising 1328 marker loci including novel 625 CKAMs, 314 TOG-SNPs and 389 published marker loci with an average inter-marker distance of 0.59 cM was constructed. Detailed analyses of 1064 mapped loci of this second-generation chickpea genetic map showed a higher degree of synteny with genome of Medicago truncatula, followed by Glycine max, Lotus japonicus and least with Vigna unguiculata. Development of these cost-effective CKAMs for SNP genotyping will be useful not only for genetics research and breeding applications in chickpea, but also for utilizing genome information from other sequenced or model legumes.

a b s t r a c tSterility mosaic disease (SMD), considered as the "green plague of pigeonpea" and caused by pigeonpea sterility mosaic virus (PPSMV) is one of the major biotic factors, which leads to heavy yield losses and hence poses a big challenge for pigeonpea production in the Indian subcontinent. Variability in the sterility mosaic pathogen revealed the occurrence of five different isolates in India. Among them, three distinct SMD isolates have been characterized, viz., Patancheru, Bangalore and Coimbatore. Molecular tools offer a viable option to tackle these biotic stresses via identification of the genomic regions associated with the trait such as SMD resistance. With an aim of identifying the gene(s)/QTLs linked with SMD resistance, two F 2 populations, i.e. ICP 8863 × ICPL 20097 (segregating for Patancheru SMD isolate) and TTB 7 × ICP 7035 (segregating for both Patancheru and Bangalore SMD isolates) were developed and F 2:3 families were phenotyped for resistance to respective isolate(s) of SMD. After screening over 3000 SSR markers on parental genotypes of each mapping population, intra-specific genetic maps comprising of 11 linkage groups and 120 and 78 SSR loci were developed for ICP 8863 × ICPL 20097 and TTB 7 × ICP 7035 populations, respectively. Composite interval mapping (CIM) based QTL analysis by using genetic mapping and phenotyping data provided four QTLs for Patancheru SMD isolate and two QTLs for Bangalore SMD isolate. Identification of different QTLs for resistance to Patancheru and Bangalore SMD isolates is an indication of involvement of different genes conferring the resistance to these two SMD isolates. One QTL namely qSMD4 identified within an interval of 2.8 cM on LG 7 explaining 24.72% of phenotypic variance, once it is validated in other genetic background, seems to be a promising QTL for use in marker assisted selection. In summary, this is the first study on development of intra-specific genetic maps and identification of QTLs for SMD resistance in pigeonpea.

The rapid increase in heat shock proteins upon exposure to damaging stresses and during plant development related to desiccation events reveal their dual importance in plant development and stress tolerance. Genome-wide sequence survey identified 20 non-redundant small heat shock proteins (sHsp) and 22 heat shock factor (Hsf) genes in barley. While all three major classes (A, B, C) of Hsfs are localized in nucleus, the 20 sHsp gene family members are localized in different cell organelles like cytoplasm, mitochondria, plastid and peroxisomes. Hsf and sHsp members are differentially regulated during drought and at different seed developmental stages suggesting the importance of chaperone role under drought as well as seed development. In silico cis-regulatory motif analysis of Hsf promoters showed an enrichment with abscisic acid responsive cis-elements (ABRE), implying regulatory role of ABA in mediating transcriptional response of HvsHsf genes. Gene regulatory network analysis identified HvHsfB2c as potential central regulator of the seed-specific expression of several HvsHsps including 17.5CI sHsp. These results indicate that HvHsfB2c is co-expressed in the central hub of small Hsps and therefore it may be regulating the expression of several HvsHsp subclasses HvHsp16.88-CI, HvHsp17.5-CI and HvHsp17.7-CI. The in vivo relevance of binding specificity of HvHsfB2C transcription factor to HSE-element present in the promoter of HvSHP17.5-CI under heat stress exposure is confirmed by gel shift and LUC-reporter assays. Further, we isolated 477 bp cDNA from barley encoding a 17.5 sHsp polypeptide, which was predominantly upregulated under drought stress treatments and also preferentially expressed in developing seeds. Recombinant HvsHsp17.5-CI protein was expressed in E. coli and purified to homogeneity, which displayed in vitro chaperone activity. The predicted structural model of HvsHsp-17.5-CI protein suggests that the α-crystallin domain is evolutionarily highly conserved.

Late embryogenesis abundant (LEA) proteins, the space fillers or molecular shields, are the hydrophilic protective proteins which play an important role during plant development and abiotic stress. The systematic survey and characterization revealed a total of 68 LEA genes, belonging to 8 families in Sorghum bicolor. The LEA-2, a typical hydrophobic family is the most abundant family. All of them are evenly distributed on all 10 chromosomes and chromosomes 1, 2, and 3 appear to be the hot spots. Majority of the S. bicolor LEA (SbLEA) genes are intron less or have fewer introns. A total of 22 paralogous events were observed and majority of them appear to be segmental duplications. Segmental duplication played an important role in SbLEA-2 family expansion. A total of 12 orthologs were observed with Arabidopsis and 13 with Oryza sativa. Majority of them are basic in nature, and targeted by chloroplast subcellular localization. Fifteen miRNAs targeted to 25 SbLEAs appear to participate in development, as well as in abiotic stress tolerance. Promoter analysis revealed the presence of abiotic stress-responsive DRE, MYB, MYC, and GT1, biotic stress-responsive W-Box, hormone-responsive ABA, ERE, and TGA, and development-responsive SKn cis-elements. This reveals that LEA proteins play a vital role during stress tolerance and developmental processes. Using microarray data, 65 SbLEA genes were analyzed in different tissues (roots, pith, rind, internode, shoot, and leaf) which show clear tissue specific expression. qRT-PCR analysis of 23 SbLEA genes revealed their abundant expression in various tissues like roots, stems and leaves. Higher expression was noticed in stems compared to roots and leaves. Majority of the SbLEA family members were up-regulated at least in one tissue under different stress conditions. The SbLEA3-2 is the regulator, which showed abundant expression under diverse stress conditions. Present study provides new insights into the formation of LEAs in S. bicolor and to understand their role in developmental processes under stress conditions, which may be a valuable source for future research.

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Members of the plant Heme Activator Protein (HAP) or NUCLEAR FACTOR Y (NF-Y) are trimeric transcription factor complexes composed of the NF-YA, NF-YB and NF-YC subfamilies. They bind to the CCAAT box in the promoter regions of the target genes and regulate gene expressions. Plant NF-Ys were reported to be involved in adaptation to several abiotic stresses as well as in development. In silico analysis of Sorghum bicolor genome resulted in the identification of a total of 42 NF-Y genes, among which 8 code for the SbNF-YA, 19 for SbNF-YB and 15 for the SbNF-YC subunits. Analysis was also performed to characterize gene structures, chromosomal distribution, duplication status, protein subcellular localizations, conserved motifs, ancestral protein sequences, miRNAs and phylogenetic tree construction. Phylogenetic relationships and ortholog predictions displayed that sorghum has additional NF-YB genes with unknown functions in comparison with Arabidopsis. Analysis of promoters revealed that they harbour many stress-related cis-elements like ABRE and HSE, but surprisingly, DRE and MYB elements were not detected in any of the subfamilies. SbNF-YA1, 2, and 6 were found upregulated under 200 mM salt and 200 mM mannitol stresses. While NF-YA7 appeared associated with high temperature (40°C) stress, NF-YA8 was triggered by both cold (4°C) and high temperature stresses. Among NF-YB genes, 7, 12, 15, and 16 were induced under multiple stress conditions such as salt, mannitol, ABA, cold and high temperatures. Likewise, NF-YC 6, 11, 12, 14, and 15 were enhanced significantly in a tissue specific manner under multiple abiotic stress conditions. Majority of the mannitol (drought)-inducible genes were also induced by salt, high temperature stresses and ABA. Few of the high temperature stress-induced genes are also induced by cold stress (NF-YA2, 4, 6, 8, NF-YB2, 7, 10, 11, 12, 14, 16, 17, NF-YC4, 6, 12, and 13) thus suggesting a cross talk among them. This work paves the way for investigating the roles of diverse sorghum NF-Y proteins during abiotic stress responses and provides an insight into the evolution of diverse NF-Y members.

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