Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes, GBSSI and SSIIa, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.

Legume-rhizobial symbiotic nitrogen fixation is the most efficient nitrogen assimilation system in the ecosystem. In the special interaction between organ–root nodules, legumes supply rhizobial carbohydrates for their proliferation, while rhizobials provide host plants with absorbable nitrogen. Nodule initiation and formation require a complex molecular dialogue between legumes and rhizobia, which involves the accurate regulation of a series of legume genes. The CCR4–NOT complex is a conserved multi-subunit complex with functions regulating gene expression in many cellular processes. However, the functions of the CCR4–NOT complex in rhizobia–host interactions remain unclear. In this study, we identified seven members of the NOT4 family in soybean and further classified them into three subgroups. Bioinformatic analysis showed that NOT4s shared relatively conserved motifs and gene structures in each subgroup, while there were significant differences between NOT4s in the different subgroups. Expression profile analysis indicated that NOT4s may be involved in nodulation in soybean, as most of them were induced by Rhizobium infection and highly expressed in nodules. We further selected GmNOT4-1 to clarify the biological function of these genes in soybean nodulation. Interestingly, we found that either GmNOT4-1 overexpression or down-regulation of GmNOT4-1 by RNAi or CRISPR/Cas9 gene editing would suppress the number of nodules in soybean. Intriguingly, alterations in the expression of GmNOT4-1 repressed the expression of genes in the Nod factor signaling pathway. This research provides new insight into the function of the CCR4–NOT family in legumes and reveals GmNOT4-1 to be a potent gene for regulating symbiotic nodulation.

Plant height is one of the most important agronomic traits that affects yield in wheat, owing to that the utilization of dwarf or semi-dwarf genes is closely associated with lodging resistance. In this study, we identified a semi-dwarf mutant, jg0030, induced by γ-ray mutagenesis of the wheat variety ‘Jing411’ (wild type). Compared with the ‘Jing411’, plant height of the jg0030 mutant was reduced by 7%-18% in two years’ field experiments, and the plants showed no changes in yield-related traits. Treatment with gibberellic acid (GA) suggested that jg0030 is a GA-sensitive mutant. Analysis of the frequency distribution of plant height in 297 F3 families derived from crossing jg0030 with the ‘Jing411’ indicated that the semi-dwarf phenotype is controlled by a major gene. Using the wheat 660K SNP array-based Bulked Segregant Analysis (BSA) and the exome capture sequencing-BSA assay, the dwarf gene was mapped on the long arm of chromosome 2B. We developed a set of KASP markers and mapped the dwarf gene to a region between marker PH1 and PH7. This region encompassed a genetic distance of 55.21 cM, corresponding to a physical distance of 98.3 Mb. The results of our study provide a new genetic resource and linked markers for wheat improvement in molecular breeding programs.

The rise in global temperature is not only affecting plant functioning directly, but is also increasing air vapour pressure deficit (VPD). The yield of banana is heavily affected by water deficit but so far breeding programs have never addressed the issue of water deficit caused by high VPD. A reduction in transpiration at high VPD has been suggested as a key drought tolerance breeding trait to avoid excessive water loss, hydraulic failure and to increase water use efficiency. In this study, stomatal and transpiration responses under increasing VPD at the leaf and whole-plant level of 8 wild banana (sub)species were evaluated, displaying significant differences in stomatal reactivity. Three different phenotypic groups were identified under increasing VPD. While (sub)species of group III maintained high transpiration rates under increasing VPD, M. acuminata ssp. errans (group I), M. acuminata ssp. zebrina (group II) and M. balbisiana (group II) showed the highest transpiration rate limitations to increasing VPD. In contrast to group I, group II only showed strong reductions at high VPD levels, limiting the cost of reduced photosynthesis and strongly increasing their water use efficiency. M. acuminata ssp. zebrina and M. balbisiana thus show the most favourable responses. This study provides a basis for the identification of potential parent material in gene banks for breeding future-proof bananas that cope better with lack of water.

Under the changing climate due to global warming, various abiotic stresses including drought (D) and salinity (S) are expected to further trigger their devastating effects on the already vulnerable crop production systems. This experiment was designed to unravel and quantify the potential role of exogenous application of salicylic acid (SA) in mitigating both D and S stresses and their combination (D+S), with three replications using CRD (Completely Randomized Design). The obtained results of the current study demonstrated significant effects of all three types of stresses (D, S, and D+S) on various parameters in Brassica napus plants. Quantifying these parameters provides a more informative and precise understanding of the findings. Current results revealed that all three stress types (D, S, and D+S) resulted in a reduction in leaf area (13.65 to 21.87%), chlorophyll levels (30 to 50%), gaseous exchange rate (30 to 54%) and the concentration of mineral ions compared to non-stressed plants. However, application of SA helped in mitigating these stresses by ameliorating the negative effects of these stresses. Moreover, Malondialdehyde (MDA) contents, an indicator of lipid per-oxidation and oxidative stress, the levels of antioxidants, proline content, an osmolyte associated with stress tolerance, and sugar content in the leaves were elevated in response to all stress conditions. In addition, the ultra-structures within the leaves were negatively affected by the stresses, while an application of SA considerably minimized the deterioration of these structures thus providing protection to the brassica plants against the stresses. In a nutshell, the findings of this study suggest that SA application in S, D and S+ D stresses provides evasion to the plants by improving different physiological and growth indices. The application of Salicylic Acid (SA) mitigated the negative effects of the stresses on all the above parameters, reducing MDA contents (47%), antioxidants (11 to 20%), proline (28%), sugar contents (20.50%), and minimizing the deterioration of ultra-structures. The findings emphasize the potential mitigatory role of SA in mitigating D and S stresses and highlight the need for further research to understand the underlying mechanisms in detail and explore its practical application in farming practices.