Enrichment of amylopectin in sub-tropically adapted maize hybrids through genomics-assisted introgression of waxy1 gene encoding granule-bound starch synthase (GBSS)

High amylopectin in waxy maize synergistically affects seed germination and seedling vigour over traditional maize genotypes

Waxy maize grains rich in amylopectin have emerged as a popular food and industrial raw materials. Here, a set of waxy inbreds having recessive waxy1 (wx1) gene derived through marker-assisted selection (MAS), and their original versions were evaluated for germination, seed vigour index-I and vigour index-II, electrical conductivity (EC) and enzymatic activities viz., dehydrogenase (DH), esterase (EST), peroxidase (POX), superoxide dismutase (SOD) and α-amylase (AMY). Waxy inbreds under study possessed average 97.8% amylopectin compared to 72.4% in original inbreds. Waxy versions showed 15.2% more test weight, 4.3% increase in germination, 22.7% higher seed vigour index-I and 28.3% higher seed vigour index-II, respectively, over the original inbreds. Further, activity of DH, EST, POX, SOD and AMY of MAS-derived waxy inbreds was more than that of original inbreds, whereas EC was less in improved inbreds compared to originals. Amylopectin exhibited strong positive correlations (r = 0.69 to 0.97**) with seed germination, vigour index-I and -II, DH, SOD, POX, EST and AMY activity. However, amylopectin showed negative correlation of - 0.82** with EC. Seed germination and seed vigour indices were also positively correlated with all enzymatic activities (r = 0.58 to 0.92**). The analysis revealed that waxy inbreds possess better seed vigour and enzymatic activities over traditional inbreds. This is the first report of synergistic effects of wx1 gene on seed germination, vigour and enzymatic activities in maize endosperm.

Characterization of Indian waxy and non-waxy maize germplasm for genetic differentiation through SNP genotyping

Waxy maize characterized by high amylopectin content resulting from a recessive wx1 gene, is important for both dietary and industrial applications, yet it suffers from low yields and limited breeding options. This study aims to develop a thorough understanding of the underlying genetics for successful hybridization experiments in waxy maize and the identification of potential cross combinations to derive high-yielding waxy maize hybrids in India. Here, we evaluated the kernel starch composition, yield-related traits, molecular diversity, kinship, LD, population structure, and selection signatures in a panel of 11 waxy and 37 non-waxy maize genotypes. The starch content in the panel ranged from 57.85 to 66.96%, while the amylopectin ranged from 70.65% to 96.32%. A significant positive correlation between kernel starch and amylopectin (0.39**) was identified suggesting the potential for simultaneous improvement of both these traits. The 48 maize lines were genotyped with 24,477 highly polymorphic single nucleotide polymorphisms (SNPs). Seventy-eight per cent of the pair-wise relative kinship values were less than or equal to 0, indicating minimal redundancy in the genomic composition of the inbred lines. The range of genetic distance among the pairs of waxy lines was 0.190 to 0.231 as compared to 0.076-0.264 in the non-waxy genotypes suggesting a greater genetic variation among the non-waxy genotypes. The mean LD value across the genome was 0.44. Two to four groups were identified using the model-based population structure, phylogenetic analysis and principal component analysis with no clear pattern of clustering based on the type of corn. Pairwise comparisons using the SNP dataset between waxy and non-waxy maize detected 27 loci under positive selection. The information generated in this study will be useful in the diversification of Indian waxy maize lines and the development of superior waxy maize hybrids.

Unraveling the interactive effect of opaque2 and waxy1 genes on kernel nutritional qualities and physical properties in maize (Zea mays L.)

The mutant waxy allele (wx1) is responsible for increased amylopectin in maize starch, with a wide range of food and industrial applications. The amino acid profile of waxy maize resembles normal maize, making it particularly deficient in lysine and tryptophan. Therefore, the present study explored the combined effects of genes governing carbohydrate and protein composition on nutritional profile and kernel physical properties by crossing Quality Protein Maize (QPM) (o2o2/wx1+wx1+) and waxy (o2+o2+/wx1wx1) parents. Selected homozygous genotypic classes from F2 populations showed that double mutants (o2o2/wx1wx1) had the highest amount of lysine (mean: 0.396%), tryptophan (mean: 0.099%), and amylopectin (mean: 98.56%) than respective single mutants (o2o2/wx1+wx1+: lysine: 0.338%, tryptophan: 0.083%, amylopectin: 74.66%; o2+o2+/wx1wx1: lysine: 0.223%, tryptophan: 0.040%, amylopectin: 95.21%). The wx1 was found to impart an enhanced effect on the lysine and tryptophan, while o2 complemented enhanced amylopectin content in the population in the o2+o2+ and wx1+wx1+ genotypic background, respectively, besides o2o2wx1wx1 genotypes. The pattern of kernel hardness observed based on average genotypic values was o2+o2+/wx1+wx1+ (401.28 N) < o2+o2+/wx1wx1 (330.99 N) < o2o2/wx1wx1 (304.28 N) < o2o2/wx1+wx1+ (210.96 N). Therefore, with the distinctive effects of wx1 and o2, improving lysine, tryptophan, and amylopectin while maintaining kernel hardness is feasible while breeding for o2o2/wx1wx1 germplasm and enhancing the utilization spectrum of waxy maize.

Comparative transcriptome profiling reveals the mechanism of increasing lysine and tryptophan content through pyramiding opaque2, opaque16 and waxy1 genes in maize

To explore the molecular mechanism behind maize grain quality and use of different gene stacking to improve the nutritional quality of grain, marker-assisted selection (MAS) was used to select three recessive mutant lines containing o2o16wx, along with the double-recessive mutant lines containing o2o16, o2wx, and o16wx. The resulting seeds were taken for transcriptome sequencing analysis 18 days after pollination (DAP). Results: Compared with the recurrent parent genes, in the lysine synthesis pathway, the gene pyramiding lines (o2o16wx, o2wx, and o16wx) revealed that the gene encoding aspartate kinase (AK) was up-regulated and promoted lysine synthesis. In the lysine degradation pathway, 'QCL8010_1' (o2o16wx) revealed that the gene encoding saccharopine dehydrogenase (LKR/SDH) was down-regulated. In addition, the gene pyramiding lines (o2o16wx, o2o16, and o16wx) indicated that the gene encoding 2-oxoglutarate dehydrogenase E1 component (OGDH) was down-regulated, inhibiting the degradation of lysine. In the tryptophan synthesis pathway, the genes encoding anthranilate synthase (AS), anthranilate synthase (APT), and tryptophan synthase (TS) were up-regulated (in o2o16wx, o2o16, o2wx, and o16wx), and promote tryptophan synthesis. In the tryptophan degradation pathway, it was revealed that the genes encoding indole-3-producing oxidase (IAAO) and indole-3-pyruvate monooxygenase (YUCCA) were down-regulated. These results provide a reference for revealing the mechanism of the o2, o16, and wx with different gene pyramiding to improve grain quality in maize.

Combining genome-wide association study and linkage mapping in the genetic dissection of amylose content in maize (Zea mays L.)

KEY MESSAGE

Integrated linkage and association analysis revealed genetic basis across multiple environments. The genes Zm00001d003102 and Zm00001d015905 were further verified to influence amylose content using gene-based association study. Maize kernel amylose is an important source of human food and industrial raw material. However, the genetic basis underlying maize amylose content is still obscure. Herein, we used an intermated B73 × Mo17 (IBM) Syn10 doubled haploid population composed of 222 lines and a germplasm set including 305 inbred lines to uncover the genetic control for amylose content under four environments. Linkage mapping detected 16 unique QTL, among which four were individually repeatedly identified across multiple environments. Genome-wide association study revealed 17 significant (P = 2.24E-06) single-nucleotide polymorphisms, of which two (SYN19568 and PZE-105090500) were located in the intervals of the mapped QTL (qAC2 and qAC5-3), respectively. According to the two population co-localized loci, 20 genes were confirmed as the candidate genes for amylose content. Gene-based association analysis indicated that the variants in Zm00001d003102 (Beta-16-galactosyltransferase GALT29A) and Zm00001d015905 (Sugar transporter 4a) affected amylose content across multi-environment. Tissue expression analysis showed that the two genes were specifically highly expressed in the ear and stem, respectively, suggesting that they might participate in sugar transport from source to sink organs. Our study provides valuable genetic information for breeding maize varieties with high amylose.

Analysis and Research on Starch Content and Its Processing, Structure and Quality of 12 Adzuki Bean Varieties

Investigating starch properties of different adzuki beans provides an important theoretical basis for its application. A comparative study was conducted to evaluate the starch content, processing, digestion, and structural quality of 12 adzuki bean varieties. The variation ranges of the 12 adzuki bean varieties with specific analyzed parameters, including the amylose/amylopectin (AM/AP) ratio, bean paste rate, water separation rate, solubility, swelling power and resistant starch (RS) content level, were 5.52-39.05%, 44.7-68.2%, 45.56-54.29%, 6.79-12.07%, 11.83-15.39%, and 2.02-14.634%, respectively. The crystallinity varied from 20.92 to 37.38%, belonging to type BC(The starch crystal type is mainly type C, supplemented by type B). In correlation analysis, red and blue represent positive and negative correlation, respectively. Correlation analysis indicated that the termination temperature of adzuki bean starch was positively correlated with AM/AP ratio. Therefore, the higher the melting temperature, the better the freeze-thaw stability. The 12 varieties were divided into Class I, Class II, and Class III by cluster analysis, based on application field. Class I was unsuitable for the diabetics' diet; Class II was suitable for a stabilizer; and Class III was suitable for bean paste, mixtures, and thickeners. The present study could provide a theoretical basis for their application in the nutritional and nutraceutical field.

Pollen staining is a rapid and cost-effective alternative to marker-assisted selection for recessive waxy1 gene governing high amylopectin in maize

Waxy maize is popular for food-, feed- and industrial usage. It possesses a recessive waxy1 (wx1) gene that enhances amylopectin to ~ 95-100%, compared to ~ 70-75% in traditional maize. Marker-assisted selection (MAS) is a preferred approach to converting normal maize into a waxy version. However, it requires specialized expertise, a well-equipped laboratory, and high cost. Here, pollen staining was used as an alternative approach to MAS. BC1F1, BC1F2 and BC2F2 populations in seven genetic backgrounds segregating for the wx1 gene were used. Pollens treated with iodine-potassium iodide showed that wild types (Wx1Wx1) were dark purple, while waxy pollens (wx1wx1) exhibited red colour. Heterozygotes (Wx1wx1) showed a mix of both dark purple and red colour. Staining of endosperm flour also confirmed the same findings. Wx1-based genotyping using phi022 and wx2507F/RG confirmed the same genotypic status. The average amylopectin among genotypes having red coloured pollens was 97.6%, while it was 72.5% among dark purple. Heterozygotes with both dark purple and red pollens had 85.2% amylopectin. Pollen staining showed complete agreement with the genotyping as well as amylopectin contents. Pollen staining saved 81% cost, and 54% time compared to MAS. This is the first report on the utilization of pollen staining for selecting the wx1 allele in segregating populations used for the development of waxy maize hybrids.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01240-1.