Evolution of Deeper Rooting 1-like homoeologs in wheat entails the C-terminus mutations as well as gain and loss of auxin response elements.

Root growth angle (RGA) in response to gravity controlled by auxin is a pertinent target trait for obtainment of higher yield in cereals. But molecular basis of this root architecture trait remain obscure in wheat and barley. We selected four cultivars two each for wheat and barley to unveil the molecular genetic mechanism of Deeper Rooting 1-like gene which controls RGA in rice leading to higher yield under drought imposition. Morphological analyses revealed a deeper and vertically oriented root growth in "NARC 2009" variety of wheat than "Galaxy" and two other barley cultivars "Scarlet" and "ISR42-8". Three new homoeologs designated as TaANDRO1-like, TaBNDRO1-like and TaDNDRO1-like corresponding to A, B and D genomes of wheat could be isolated from "NARC 2009". Due to frameshift and intronization/exonization events the gene structures of these paralogs exhibit variations in size. DRO1-like genes with five distinct domains prevail in diverse plant phyla from mosses to angiosperms but in lower plants their differentiation from LAZY, NGR and TAC1 (root and shoot angle genes) is enigmatic. Instead of IGT as denominator motif of this family, a new C-terminus motif WxxTD in the V-domain is proposed as family specific motif. The EAR-like motif IVLEM at the C-terminus of the TaADRO1-like and TaDDRO1-like that diverged to KLHTLIPNK in TaBDRO1-like and HvDRO1-like is the hallmark of these proteins. Split-YFP and yeast two hybrid assays complemented the interaction of TaDRO1-like with TOPLESS-a repressor of auxin regulated root promoting genes in plants-through IVLEM/KLHTLIPNK motif. Quantitative RT-PCR revealed abundance of DRO1-like RNA in root tips and spikelets while transcript signals were barely detectable in shoot and leaf tissues. Interestingly, wheat exhibited stronger expression of TaBDRO1-like than barley (HvDRO1-like), but TaBDRO1-like was the least expressing among three paralogs. The underlying cause of this expression divergence seems to be the presence of AuxRE motif TGTCTC and core TGTC with a coupling AuxRE-like motif ATTTTCTT proximal to the transcriptional start site in TaBDRO1-like and HvDRO1-like promoters. This is evident from binding of ARF1 to TGTCTC and TGTC motifs of TaBDRO1-like as revealed by yeast one-hybrid assay. Thus, evolution of DRO1-like wheat homoeologs might incorporate the C-terminus mutations as well as gain and loss of AuxREs and other cis-regulatory elements during expression divergence. Since root architecture is an important target trait for wheat crop improvement, therefore DRO1-like genes have potential applications in plant breeding for enhancement of plant productivity by the use of modern genome editing approaches.

An Ancestral Allele of Pyrroline-5-carboxylate synthase1 Promotes Proline Accumulation and Drought Adaptation in Cultivated Barley.

Water scarcity is a critical threat to global crop production. Here, we used the natural diversity of barley (Hordeum vulgare) to dissect the genetic control of proline (Pro) mediated drought stress adaptation. Genetic mapping and positional cloning of a major drought-inducible quantitative trait locus (QPro.S42-1H) revealed unique allelic variation in pyrroline-5-carboxylate synthase (P5cs1) between the cultivated cultivar Scarlett (ssp. vulgare) and the wild barley accession ISR42-8 (ssp. spontaneum). The putative causative mutations were located in the promoter of P5cs1 across the DNA binding motifs for abscisic acid-responsive element binding transcription factors. Introgression line (IL) S42IL-143 carrying the wild allele of P5cs1 showed significant up-regulation of P5cs1 expression compared to Scarlett, which was consistent with variation in Pro accumulation under drought. Next, we transiently expressed promoter::reporter constructs of ISR42-8 and Scarlett alleles in Arabidopsis (Arabidopsis thaliana) mesophyll protoplasts. GUS expression analysis showed a significantly higher activation of the ISR42-8 promoter compared to Scarlett upon abscisic acid treatment. Notably, the ISR42-8 promoter activity was impaired in protoplasts isolated from the loss-of-function abf1abf2abf3abf4 quadruple mutant. A series of phenotypic evaluations demonstrated that S42IL-143 maintained leaf water content and photosynthetic activity longer than Scarlett under drought. These findings suggest that the ancestral variant of P5cs1 has the potential for drought tolerance and understanding drought physiology of barley and related crops.

Correction: Genetic Mapping Reveals Broader Role of Vrn-H3 Gene in Root and Shoot Development beyond Heading in Barley.

[This corrects the article DOI: 10.1371/journal.pone.0158718.].

Genetic Mapping Reveals Broader Role of Vrn-H3 Gene in Root and Shoot Development beyond Heading in Barley.

The aim of the present study was to dissect the genetic inheritance and interplay of root, shoot and heading attributes for a better understanding of these traits in crop production. For this, we utilized quantitative trait loci (QTL) and candidate gene analysis approach using a second filial (F2) population originated from a cross between spring cultivar Cheri and wild barley accession ICB181160. The F2 population comprising 182 plants was phenotyped for root dry weight (RDW), root volume (RV), root length (RL) and shoot dry weight (SDW), tiller number per plant (TIL) and days to heading (HEA). In parallel, this population was genotyped using polymerase chain reaction (PCR) based cleaved amplified polymorphic sequence (CAPS) markers distributed across the whole genome. Marker by trait analysis revealed 16 QTL for root and shoot traits localized on chromosomes 1H, 3H, 4H, 5H and 7H. The strongest and a common QTL effect for root, shoot and heading traits was identified on chromosome 7H at the putative region of Vrn-H3 gene. Later, we have established PCR based gene specific marker HvVrnH3 revealing polymorphism for early heading Vrn-H3 allele in Cheri and late heading allele vrn-H3 in ICB181160. Genotyping of these alleles revealed a clear co-segregation of early heading Vrn-H3 allele with lower root and shoot attributes, while late heading vrn-H3 allele with more TIL and higher root biomass suggesting a primary insight on the function of Vrn-H3 gene beyond flowering. Genetic interactions of vernalization genes Vrn-H3 with Vrn-H2 and Vrn-H1 also suggested the major role of Vrn-H3 alleles in determining root and shoot trait variations in barley. We believe, these data provide an opportunity for further research to test a precise significance of early heading on yield components and root associated sustainability in crops like barley and wheat.

Wild barley introgression lines revealed novel QTL alleles for root and related shoot traits in the cultivated barley (Hordeum vulgare L.).

BACKGROUND: Root is the prime organ that sucks water and nutrients from deep layer of soil. Wild barley diversity exhibits remarkable variation in root system architecture that seems crucial in its adaptation to abiotic stresses like drought. In the present study, we performed quantitative trait locus (QTL) mapping of root and related shoot traits under control and drought conditions using a population of wild barley introgression lines (ILs). This population (S42IL) comprising of genome-wide introgressions of wild barley accession ISR42-8 in the cultivar Scarlett background. Here, we aimed to detect novel QTL alleles for improved root and related shoot features and to introduce them in modern cultivars. RESULTS: The cultivar Scarlett and wild barley accession ISR42-8 revealed significant variation of root and related shoot traits. ISR42-8 showed a higher performance in root system attributes like root dry weight (RDW), root volume (RV), root length (RL) and tiller number per plant (TIL) than Scarlett. Whereas, Scarlett exhibited erect type growth habit (GH) as compared to spreading growth habit in ISR42-8. The S42IL population revealed significant and wide range of variation for the investigated traits. Strong positive correlations were found among the root related traits whereas GH revealed negative correlation with root and shoot traits. The trait-wise comparison of phenotypic data with the ILs genetic map revealed six, eight, five, five and four QTL for RL, RDW, RV, TIL and GH, respectively. These QTL were linked to one or several traits simultaneously and localized to 15 regions across all chromosomes. Among these, beneficial QTL alleles of wild origin for RL, RDW, RV, TIL and GH, have been fixed in the cultivar Scarlett background. CONCLUSIONS: The present study revealed 15 chromosomal regions where the exotic QTL alleles showed improvement for root and related shoot traits. These data suggest that wild barley accession ISR42-8 bears alleles different from those of Scarlett. Hence, the utility of genome-wide wild barley introgression lines is desirable to test the performance of individual exotic alleles in the elite gene pool as well as to transfer them in the cultivated germplasm.