Dataset Information

Identification of Gene Associated with Sweetness in Corn (Zea mays L.) by Genome-Wide Association Study (GWAS) and Development of a Functional SNP Marker for Predicting Sweet Corn.

ABSTRACT: Sweetness is an economically important eating quality trait for sweet-corn breeding. To investigate the genetic control of the sweetness trait, we conducted a genome-wide association study (GWAS) in an association panel consisting of 250 sweet corn and waxy corn inbred and recombinant inbred lines (RILs), together with the genotypes obtained from the high-density 600K maize genotyping single-nucleotide polymorphism (SNP) array. GWAS results identified 12 significantly associated SNPs on chromosomes 3, 4, 5, and 7. The most associated SNP, AX_91849634, was found on chromosome 3 with a highly significant p-value of ≤1.53 × 10-14. The candidate gene identified within the linkage disequilibrium (LD) of this marker was shrunken2 (Zm00001d044129; sh2), which encodes ADP-glucose pyrophosphorylase (AGPase), a 60 kDa subunit enzyme that affects starch metabolism in the maize endosperm. Several SNP markers specific to variants in sh2 were developed and validated. According to the validation in a set of 81 inbred, RIL, and popular corn varieties, marker Sh2_rs844805326, which was developed on the basis of the SNP at the position 154 of exon 1, was highly efficient in classifying sh2-based sweet corn from other types of corn. This functional marker is extremely useful for marker-assisted breeding in sh2-sweet corn improvement and marketable seed production.

SUBMITTER: Ruanjaichon V

PROVIDER: S-EPMC8235792 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Publications

Identification of Gene Associated with Sweetness in Corn (<i>Zea mays</i> L.) by Genome-Wide Association Study (GWAS) and Development of a Functional SNP Marker for Predicting Sweet Corn.

Ruanjaichon Vinitchan V Khammona Kanogporn K Thunnom Burin B Suriharn Khundej K Kerdsri Chalong C Aesomnuk Wanchana W Yongsuwan Arweewut A Chaomueang Naraporn N Thammapichai Paradee P Arikit Siwaret S Wanchana Samart S Toojinda Theerayut T

Plants (Basel, Switzerland) 20210618 6

Sweetness is an economically important eating quality trait for sweet-corn breeding. To investigate the genetic control of the sweetness trait, we conducted a genome-wide association study (GWAS) in an association panel consisting of 250 sweet corn and waxy corn inbred and recombinant inbred lines (RILs), together with the genotypes obtained from the high-density 600K maize genotyping single-nucleotide polymorphism (SNP) array. GWAS results identified 12 significantly associated SNPs on chromoso ...[more]

PMID: 34207135

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Project description:Accumulation of stress ethylene in plants due to osmotic stress is a major challenge for the achievement of optimum sweet corn crop yield with limited availability of irrigation water. A significant increase in earth's temperature is also making the conditions more crucial regarding the availability of ample quantity of irrigation water for crops production. Plant growth promoting rhizobacteria (PGPR) can play an imperative role in this regard. Inoculation of rhizobacteria can provide resistance and adaptability to crops against osmotic stress. In addition, these rhizobacteria also have potential to solve future food security issues. That's why the current study was planned to examine the efficacious functioning of Pseudomonas fluorescens strains on yields and physiological characteristics of sweet corn (Zea mays L. var saccharata) under different levels of irrigation. Three irrigation levels i.e., 100% (I100 no stress), 80% (I80), and 60% (I60) were used during sweet corn cultivation. However, there were four rhizobacteria strains i.e., P. fluorescens P1, P. fluorescens P3, P. fluorescens P8, P. fluorescens P14 which were used in the experiment. The results showed that severe water stress (60% of plant water requirement) decreased chlorophyll a, chlorophyll b, and total chlorophyll contents, Fv/Fm ratio and nutrients uptake. A significant increase in F0, Fm, proline, total soluble sugars, catalase (CAT) and peroxidase (POX) activity led to less ear yield and canned seed yield. Combination of four strains significantly increased the yield traits of sweet corn i.e., ear and (44%) and canned seed yield (27%) over control. The highest promoting effect was observed in the combination of four strains treatment and followed by P1 strain in reducing the harmful effects of drought stress and improving sweet corn productivity. However, P14 gave minimum improvement in growth and yield indices under limited availability of water. In conclusion, combination of four strains inoculation is an efficacious approach for the achievement of better yield of sweet corn under osmotic stress.

Project description:Global environmental changes with more extreme episodes of heat waves are major threats to agricultural productivity. Heat stress in spring affects the reproductive stage of maize, resulting in tassel blast, pollen abortion, poor pollination, reduced seed set, barren ears and ultimately yield loss. As an aneamophelous crop, maize has a propensity for pollen abortion under heat stress conditions. To overcome the existing challenges of heat stress and pollen abortion, this study utilized a broad genetic base of maize germplasm to identify superior alleles to be utilized in breeding programs. A panel of 375 inbred lines was morpho-physiologically screened under normal and heat stress conditions in two locations across two consecutive planting seasons, 2017 and 2018. The exposure of pollen to high temperature showed drastic decline in pollen germination percentage. The average pollen germination percentage (PGP) at 35 and 45°C was 40.3% and 9.7%, respectively, an average decline of 30.6%. A subset of 275 inbred lines were sequenced using tunable genotyping by sequencing, resulting in 170,098 single nucleotide polymorphisms (SNPs) after filtration. Genome wide association of PGP in a subset of 122 inbred lines resulted in ten SNPs associated with PGP35°C (p ≤ 10-5), nine with PGP45°C (p ≤ 10-6-10-8) and ten SNPs associated with PGP ratio (p ≤ 10-5). No SNPs were found to be in common across PGP traits. The number of favorable alleles possessed by each inbred line for PGP35°C, PGP45°C, and the PGP ratio ranged between 4 and 10, 3-13 and 5-13, respectively. In contrast, the number of negative alleles for these traits ranged between 2 and 8, 3-13 and 3-13, respectively. Genetic mapping of yield (adjusted weight per plant, AWP-1) and flowering time (anthesis-silking interval, ASI) in 275 lines revealed five common SNPs: three shared for AWP-1 between normal and heat stress conditions, one for ASI between conditions, and one SNP, CM007648.1-86615409, was associated with both ASI and AWP-1. Variety selection can be performed based on these favorable alleles for various traits. These marker trait associations identified in the diversity panel can be utilized in breeding programs to improve heat stress tolerance in maize.

Dataset Information

Identification of Gene Associated with Sweetness in Corn (Zea mays L.) by Genome-Wide Association Study (GWAS) and Development of a Functional SNP Marker for Predicting Sweet Corn.

Publications

Identification of Gene Associated with Sweetness in Corn (<i>Zea mays</i> L.) by Genome-Wide Association Study (GWAS) and Development of a Functional SNP Marker for Predicting Sweet Corn.

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