Elucidating the interactive impact of tillage, residue retention and system intensification on pearl millet yield stability and biofortification under rainfed agro-ecosystems

Micronutrient malnutrition and suboptimal yields pose significant challenges in rainfed cropping systems worldwide. To address these issues, the implementation of climate-smart management strategies such as conservation agriculture (CA) and system intensification of millet cropping systems is crucial. In this study, we investigated the effects of different system intensification options, residue management, and contrasting tillage practices on pearl millet yield stability, biofortification, and the fatty acid profile of the pearl millet. ZT systems with intercropping of legumes (cluster bean, cowpea, and chickpea) significantly increased productivity (7–12.5%), micronutrient biofortification [Fe (12.5%), Zn (4.9–12.2%), Mn (3.1–6.7%), and Cu (8.3–16.7%)], protein content (2.2–9.9%), oil content (1.3%), and fatty acid profile of pearl millet grains compared to conventional tillage (CT)-based systems with sole cropping. The interactive effect of tillage, residue retention, and system intensification analyzed using GGE statistical analysis revealed that the best combination for achieving stable yields and micronutrient fortification was residue retention in both (wet and dry) seasons coupled with a ZT pearl millet + cowpea–mustard (both with and without barley intercropping) system. In conclusion, ZT combined with residue recycling and legume intercropping can be recommended as an effective approach to achieve stable yield levels and enhance the biofortification of pearl millet in rainfed agroecosystems of South Asia

Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat

A large portion of the global wheat crop is milled to produce flour for use in the production of foods such as bread. Pressure to increase food supplies sustainably can be address directly by reducing post-harvest losses during processes such as flour milling. The recovery of flour in the milling of wheat is genetically determined but difficult to assess in wheat breeding due to the requirement for a large sample. Here we report the discovery that human selection for altered expression of putative cell adhesion proteins is associated with wheats that give high yields of flour on milling. Genes encoding fasciclin-like arabinogalactan proteins are expressed at low levels in high milling wheat genotypes at mid grain development. Thirty worldwide wheat genotypes were grouped into good and poor millers based flour yield obtained from laboratory scale milling of mature seeds. Differentially expressed genes were identified by comparing transcript profiles at 14 and 30 days post anthesis obtained from RNA-seq data of all the genotypes. Direct selection for genotypes with appropriate expression of these genes will greatly accelerate wheat breeding and ensure high recoveries of flour from wheat by resulting in grains that break up more easily on milling

Influence of gene expression on hardness in wheat

Puroindoline (Pina and Pinb) genes control grain texture or hardness in wheat. Wild-type/ soft alleles lead to softer grain while a mutation in one or both of these genes results in a hard grain. Variation in hardness in genotypes with identical Pin alleles (wild-type or mutant) is known but the molecular basis of this is not known. We now report the identification of wheat genotypes with hard grain texture and wild-type/soft Pin alleles indicating that hardness in wheat may be controlled by factors other than mutations in the coding region of the Pin genes. RNA-Seq analysis was used to determine the variation in the transcriptome of developing grains of thirty three diverse wheat genotypes including hard (mutant Pin) and soft (wild type) and those that were hard without having Pin mutations. This defined the role of pin gene expression and identified other candidate genes associated with hardness. Pina was not expressed in hard wheat with a mutation in the Pina gene. The ratio of Pina to Pinb expression was generally lower in the hard non mutant genotypes. Hardness may be associated with differences in Pin expression and other factors and is not simply associated with mutations in the PIN protein coding sequences

Analysis of the expression of transcription factors and other genes associated with aleurone layer development in wheat endosperm

Defective kernel1 (dek1), crinkly4 (cr4) and supernumerary aleurone layer 1 (sal1) have been suggested as key genes involved in aleurone differentiation in cereals. Transcription factors (TFs) may play a role in regulation of aleurone development by controlling the expression of genes involved in this process. In this study, expression patterns of TFs in developing aleurone and starchy endosperm tissues of wheat was studied using RNA-Seq. Transcript profiles were obtained for aleurone and starchy endosperm tissues of the cultivar Banks at 6, 9 and 14 days post anthesis (DPA). The M-type, MIKC, MYB, CSD and NF-Y TF families were highly up-regulated, in the aleurone while in the starchy endosperm, PLATZ and Dof families were significantly up-regulated. Cr4 and sal1 homologs were identified on chromosomes 7AL, 7BL and 7DL. Dek1 was identified on chromosomes 6AL, 6BL and 6DL. Expression of dek1, cr4, sal1 and risbz1 was higher at the earlier stages of seed development. Further, we observed, sub-genome level partitioning of dek1 expression, with B and D sub-genome dek1 alleles abundantly expressed at all three stages of aleurone development. Expression of sal1 was significantly higher than that of dek1 and cr4. Aleurone development is probably regulated by several epistatic genes in wheat

Expression of the <i>Pina</i> and <i>Pinb</i> genes in developing seeds of several wheat genotypes.

<p>a,b gene expression data at 14 and 30 days post anthesis (dpa), respectively; RPKM, reads per kilo base per million mapped reads. Details in brackets after genotype names on the X-axis indicates grain hardness index and endosperm texture of genotypes classified as hard (H) or soft (S) wheats. Genotypes with HI above 50 were classified as Hard. Wheat genotypes in each group are arranged left to right with respect to increasing hardness index. Boxes on the top indicate <i>Pin</i> alleles present in the genotypes. cDNA prepared from RNA extracted from developing wheat seeds at 14 DPA, was subjected to next generation sequencing. RNA-seq analysis was undertaken using CLC Genomic Workbench V8 to determine gene expression of <i>Pina</i> and <i>Pinb</i>. The star symbol indicates data not available.</p

Expression of the <i>Pina</i> and <i>Pinb</i> genes in developing seeds of several wheat genotypes.

<p>a,b gene expression data at 14 and 30 days post anthesis (dpa), respectively; RPKM, reads per kilo base per million mapped reads. Details in brackets after genotype names on the X-axis indicates grain hardness index and endosperm texture of genotypes classified as hard (H) or soft (S) wheats. Genotypes with HI above 50 were classified as Hard. Wheat genotypes in each group are arranged left to right with respect to increasing hardness index. Boxes on the top indicate <i>Pin</i> alleles present in the genotypes. cDNA prepared from RNA extracted from developing wheat seeds at 14 DPA, was subjected to next generation sequencing. RNA-seq analysis was undertaken using CLC Genomic Workbench V8 to determine gene expression of <i>Pina</i> and <i>Pinb</i>. The star symbol indicates data not available.</p

Grain hardness Index (HI) based on presence of Pin alleles genotypes were grouped into three different groups.

<p>SD—Standard deviation.</p

Differentially expressed genes identified in the hard wheats when compared to the soft wheats.

<p>2a. Soft vs HNM+HPAM+HPBM, 2b. Soft vs HPAM, 2c. Soft vs HPBM, 2d Soft vs HNM.</p

Expression of the <i>Pinb-2</i>A, -2B, -2D genes in developing seeds of several wheat genotypes.

<p>a, b gene expression data at 14 and 30 days post anthesis (dpa) respectively; RPKM, reads per kilo base per million mapped reads. Boxes on the top indicate <i>Pin</i> alleles present in the genotypes. Details in brackets after genotype names on the X-axis indicates grain hardness index and endosperm texture of genotypes classified as hard (H) or soft (S) wheats. The asterisk indicates data not available.</p

Top down-regulated and up-regulated differentially expressed genes identified in HPAM (3a) and HPBM (3b) when compared to HNM group.

<p>Top down-regulated and up-regulated differentially expressed genes identified in HPAM (3a) and HPBM (3b) when compared to HNM group.</p