QTL identification of kernel composition traits with popcorn using both F2:3 and BC2F2 populations developed from the same cross

Genome-wide association analysis of kernel nutritional quality in two natural maize populations

As one of the three staple crops, nutritional traits in maize are important for human and animal nutrition. Grain quality-related traits are closely related to grain commercial value. Understanding the genetic basis of quality-related traits in maize would be helpful for breeding high-quality maize varieties. In this study, two association panels (AM122 and AM180) were subjected to genome-wide association analysis of grain quality-related traits, including protein content, oil content, starch content, and fiber content. In total, 98 SNPs (P < 1 × 10-4) were identified to be significantly associated with these four grain quality-related traits. By integrating two sets of public transcriptome data, 31 genes located in 200 kb regions flanking the associated SNP showed high expression during kernel development and were differentially expressed in two maize inbred lines, KA225 and KB035, with significantly different quality. These genes might regulate maize grain quality by participating in plant hormone processes, autophagy processes, and others. All these results could provide important reference information for breeding high‑quality maize varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01360-w.

Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers

The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses-Q + K and PCA + K mixed linear models (MLMs)-and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker-trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits.

Genetic dissection of QTLs for oil content in four maize DH populations

Oil is one of the main components in maize kernels. Increasing the total oil content (TOC) is favorable to optimize feeding requirement by improving maize quality. To better understand the genetic basis of TOC, quantitative trait loci (QTL) in four double haploid (DH) populations were explored. TOC exhibited continuously and approximately normal distribution in the four populations. The moderate to high broad-sense heritability (67.00-86.60%) indicated that the majority of TOC variations are controlled by genetic factors. A total of 16 QTLs were identified across all chromosomes in a range of 3.49-30.84% in term of phenotypic variation explained. Among them, six QTLs were identified as the major QTLs that explained phenotypic variation larger than 10%. Especially, qOC-1-3 and qOC-2-3 on chromosome 9 were recognized as the largest effect QTLs with 30.84% and 21.74% of phenotypic variance, respectively. Seventeen well-known genes involved in fatty acid metabolic pathway located within QTL intervals. These QTLs will enhance our understanding of the genetic basis of TOC in maize and offer prospective routes to clone candidate genes regulating TOC for breeding program to cultivate maize varieties with the better grain quality.

Nutritional Diversity in Native Germplasm of Maize Collected From Three Different Fragile Ecosystems of India

Native germplasm resources are adapted to specific ecological niches. They have sustained over generations owing to the preference of local communities for their unique taste, the utility to particular dishes, and the low cost of cultivation. They may help eradicate malnutrition and act as a source for trait-linked genes. The present dataset comprises thirty-three native germplasm of maize collected from Rajasthan, Himachal Pradesh, and Andhra Pradesh states of India with an altitudinal variation of 386–2,028 m. They were evaluated for proximate composition, minerals, nutritional attributes, and antioxidant activity and compared with the standard values reported in the Indian Food Composition Table 2017 (IFCT2017). The nutritional profile showed moisture content in the range of 7.16–10.9%, ash 0.73–1.93%, crude protein 8.68–12.0%, crude fat 3.72–8.03%, dietary fiber 5.21–11.2%, and available carbohydrates 60.6–69.8%. Three accessions, namely, Malan 11 (7.06%), Malan 24 (7.20%), and Yellow Chamba Local 02 (8.03%) exhibited almost double the crude fat content as compared with the values notified in IFCT2017 (3.77). Total sugar content obtained was in the range of 5.00–11.3%, whereas the starch content was found between 50.9 and 64.9%. All the germplasm except Yellow Chamba Local reflected a higher protein content than reported values in IFCT2017 (8.80). Sathi, Safed Chamba Local, and Ragal Makka had nearly 12% protein content. Mineral malnutrition, mainly due to iron (Fe) deficiency, is a worldwide issue to science, humanity, and society. The mineral profile revealed that most germplasm had a higher iron content. Accessions with the iron content of nearly three times of IFCT2017 reported value were identified in germplasm belonging to three states. A negative relationship was observed between the altitude of the sample collection site and available carbohydrate content. In contrast, available carbohydrate showed inverse correlations with dietary fiber, protein, and fat content. The information generated in this study can be utilized to promote these germplasm as nutrifood, nutritional surveillance, labeling, and crop improvement programs.

Genetic dissection of QTLs for starch content in four maize DH populations

Starch is the principal carbohydrate source in maize kernels. Understanding the genetic basis of starch content (SC) benefits greatly in improving maize yield and optimizing end-use quality. Here, four double haploid (DH) populations were generated and were used to identify quantitative trait loci (QTLs) associated with SC. The phenotype of SC exhibited continuous and approximate normal distribution in each population. A total of 13 QTLs for SC in maize kernels was detected in a range of 3.65-16.18% of phenotypic variation explained (PVE). Among those, only some partly overlapped with QTLs previously known to be related to SC. Meanwhile, 12 genes involved in starch synthesis and metabolism located within QTLs were identified in this study. These QTLs will lay the foundation to explore candidate genes regulating SC in maize kernel and facilitate the application of molecular marker-assisted selection for a breeding program to cultivate maize varieties with a deal of grain quality.

Genetic basis of kernel starch content decoded in a maize multi-parent population

Starch is the most abundant storage carbohydrate in maize kernels and provides calories for humans and other animals as well as raw materials for various industrial applications. Decoding the genetic basis of natural variation in kernel starch content is needed to manipulate starch quantity and quality via molecular breeding to meet future needs. Here, we identified 50 unique single quantitative trait loci (QTLs) for starch content with 18 novel QTLs via single linkage mapping, joint linkage mapping and a genome-wide association study in a multi-parent population containing six recombinant inbred line populations. Only five QTLs explained over 10% of phenotypic variation in single populations. In addition to a few large-effect and many small-effect additive QTLs, limited pairs of epistatic QTLs also contributed to the genetic basis of the variation in kernel starch content. A regional association study identified five non-starch-pathway genes that were the causal candidate genes underlying the identified QTLs for starch content. The pathway-driven analysis identified ZmTPS9, which encodes a trehalose-6-phosphate synthase in the trehalose pathway, as the causal gene for the QTL qSTA4-2, which was detected by all three statistical analyses. Knockout of ZmTPS9 increased kernel starch content and, in turn, kernel weight in maize, suggesting potential applications for ZmTPS9 in maize starch and yield improvement. These findings extend our knowledge about the genetic basis of starch content in maize kernels and provide valuable information for maize genetic improvement of starch quantity and quality.

Analysis of Nutritional Quality Attributes and Their Inter-Relationship in Maize Inbred Lines for Sustainable Livelihood

The present investigation was planned to understand the variability and inter-relationship among various nutritional quality attributes of maize kernels to identify potential donors of the respective traits for future hybridization programs. Sixty-three maize inbred lines were processed for the estimation of protein, starch, fat, sugar, 100-kernel weight, specific gravity, and moisture level of the grain. The results reveal that a wide variability among protein, starch, 100-kernel weight, specific gravity, and fat was seen, with special emphasis on the protein concentration that varied from 8.83 to 15.54%, starch (67.43–75.31%), and 100-kernel weight (9.14–36.11 gm). Factor analysis revealed that the protein concentration, starch, and 100-kernel weight, the three major components, comprise 68.58% of the kernel variability. Protein exhibited a significant negative correlation with starch and 100-kernel weight, indicating that an increase in the protein concentration will down-regulate the starch and 100-kernel weight. The inbred lines are proposed as donors for the development of high cultivars for their respective traits, viz., high protein (DMR WNC NY 403 and DMR WNC NY 404), high starch concentration (DMR WNC NY 2163, DMR WNC NY 2219, DMR WNC NY 2234, DMR WNC NY 2408, DMR WNC NY 2437, and DMR WNC NY 2466), high 100-kernel wt. (DMR WNC NY 2113, DMR WNC NY 2213, DMR WNC NY 2233, DMR WNC NY 2234, DMR WNC NY 2414, DMR WNC NY 2435, DMR WNC NY 2465, and DMR WNC NY 2474), sugar (DMR WNC NY 2417), and specific gravity (DMR WNC NY 2418). Genetic distance analysis revealed that DMR WNC NY 397 and DMR WNC NY 404 are the farthest apart inbred lines, having major differences in their protein, fat, starch, and sugar contents, followed by DMR WNC NY 2436 and DMR WNC NY 2394, DMR WNC NY 2212 and DMR WNC NY 2430, DMR WNC NY 396 and DMR WNC NY 2415, DMR WNC NY 404 and DMR WNC NY 2144, and DMR WNC NY403 and DMR WNC NY 2115. Moreover, this study proposes that these possible combinations of lines (in a breeding program) would result in genetic variability with simultaneous high values for the respective characteristics.

Genome-wide association studies of grain quality traits in maize

High quality is the main goal of today's maize breeding and the investigation of grain quality traits would help to breed high-quality varieties in maize. In this study, genome-wide association studies in a set of 248 diverse inbred lines were performed with 83,057 single nucleotide polymorphisms (SNPs), and five grain quality traits were investigated in diverse environments for two years. The results showed that maize inbred lines showed substantial natural variations of grain quality and these traits showed high broad-sense heritability. A total of 49 SNPs were found to be significantly associated with grain quality traits. Among these SNPs, four co-localized sites were commonly detected by multiple traits. The candidate genes which were searched for can be classified into 11 biological processes, 13 cellular components, and 6 molecular functions. Finally, we found 29 grain quality-related genes. These genes and the SNPs identified in the study would offer essential information for high-quality varieties breeding programs in maize.

A method to establish an "immortalized F2 " sporophyte population in the economic brown alga Undaria pinnatifida (Laminariales: Alariaceae)

Studies of quantitative trait loci based on genetic linkage maps require the establishment of a mapping population. Permanent mapping populations are more ideal than temporary ones because they can be used repeatedly. However, there has been no reported permanent sporophyte population of economically important kelp species. Based on the characteristics of the kelp life cycle, we proposed a method to establish, and then constructed experimentally, an "immortalized F2 " (IF2 ) population of Undaria pinnatifida. Doubled-haploid "female" and "male" sporophytes were obtained through the parthenogenesis of a female gametophyte clone and the selfing of a "monoicous" gametophyte clone (originally male), respectively, and they were used as the parents. The F1 hybrid line was generated by crossing the female and male gametophytes derived from the respective female and male parents. Full-sibling F2 gametophyte clones, consisting of 260 females and 260 males, were established from an F1 hybrid sporophyte. Thirty-five females and 35 males were randomly selected and paired to give rise to an IF2 population containing 35 crossing lines. A parentage analysis using 10 microsatellite markers confirmed the accuracy of the IF2 population and indicated the feasibility of this method. This proposed method may be adapted for use in other kelp species, and thus, it will be useful for genetic studies of kelp.

Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.

Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population

BACKGROUND

Starch from maize kernels has diverse applications in human and animal diets and in industry and manufacturing. To meet the demands of these applications, starch quantity and quality need improvement, which requires a clear understanding of the functional mechanisms involved in starch biosynthesis and accumulation. In this study, a recombinant inbred line (RIL) population was developed from a cross between inbred lines CI7 and K22. The RIL population, along with both parents, was grown in three environments, and then genotyped using the MaizeSNP50 BeadChip and phenotyped to dissect the genetic architecture of starch content in maize kernels.

RESULTS

Based on the genetic linkage map constructed using 2,386 bins as markers, six quantitative trait loci (QTLs) for starch content in maize kernels were detected in the CI7/K22 RIL population. Each QTL accounted for 4.7% (qSTA9-1) to 10.6% (qSTA4-1) of the starch variation. The QTL interval was further reduced using the bin-map method, with the physical distance of a single bin at the QTL peak ranging from 81.7 kb to 2.2 Mb. Based on the functional annotations and prior knowledge of the genes in the top bin, seven genes were considered as potential candidate genes for the identified QTLs. Three of the genes encode enzymes in non-starch metabolism but may indirectly affect starch biosynthesis, and four genes may act as regulators of starch biosynthesis.

CONCLUSIONS

A few large-effect QTLs, together with a certain number of minor-effect QTLs, mainly contribute to the genetic architecture of kernel starch content in our maize biparental linkage population. All of the identified QTLs, especially the large-effect QTL, qSTA4-1, with a small QTL interval, will be useful for improving the maize kernel starch content through molecular breeding.

Verification of QTL for grain starch content and its genetic correlation with oil content using two connected RIL populations in high-oil maize

Grain oil content is negatively correlated with starch content in maize in general. In this study, 282 and 263 recombinant inbred lines (RIL) developed from two crosses between one high-oil maize inbred and two normal dent maize inbreds were evaluated for grain starch content and its correlation with oil content under four environments. Single-trait QTL for starch content in single-population and joint-population analysis, and multiple-trait QTL for both starch and oil content were detected, and compared with the result obtained in the two related F(2∶3) populations. Totally, 20 single-population QTL for grain starch content were detected. No QTL was simultaneously detected across all ten cases. QTL at bins 5.03 and 9.03 were all detected in both populations and in 4 and 5 cases, respectively. Only 2 of the 16 joint-population QTL had significant effects in both populations. Three single-population QTL and 8 joint-population QTL at bins 1.03, 1.04-1.05, 3.05, 8.04-8.05, 9.03, and 9.05 could be considered as fine-mapped. Common QTL across F(2∶3) and RIL generations were observed at bins 5.04, 8.04 and 8.05 in population 1 (Pop.1), and at bin 5.03 in population 2 (Pop.2). QTL at bins 3.02-3.03, 3.05, 8.04-8.05 and 9.03 should be focused in high-starch maize breeding. In multiple-trait QTL analysis, 17 starch-oil QTL were detected, 10 in Pop.1 and 7 in Pop.2. And 22 single-trait QTL failed to show significance in multiple-trait analysis, 13 QTL for starch content and 9 QTL for oil content. However, QTL at bins 1.03, 6.03-6.04 and 8.03-8.04 might increase grain starch content and/or grain oil content without reduction in another trait. Further research should be conducted to validate the effect of these QTL in the simultaneous improvement of grain starch and oil content in maize.

QTL consistency and meta-analysis for grain yield components in three generations in maize

Grain yield is the most important and complex trait in maize. In this study, a total of 258 F(9) recombinant inbred lines (RIL), derived from a cross between dent corn inbred Dan232 and popcorn inbred N04, were evaluated for eight grain yield components under four environments. Quantitative trait loci (QTL) and their epistatic interactions were detected for all traits under each environment and in combined analysis. Meta-analysis was used to integrate genetic maps and detected QTL across three generations (RIL, F(2:3) and BC(2)F(2)) derived from the same cross. In total, 103 QTL, 42 pairs of epistatic interactions and 16 meta-QTL (mQTL) were detected. Twelve out of 13 QTL with contributions (R(2)) over 15% were consistently detected in 3-4 environments (or in combined analysis) and integrated in mQTL. Only q100GW-7-1 was detected in all four environments and in combined analysis. 100qGW-1-1 had the largest R(2) (19.3-24.6%) in three environments and in combined analysis. In contrast, 35 QTL for 6 grain yield components were detected in the BC(2)F(2) and F(2:3) generations, no common QTL across three generations were located in the same marker intervals. Only 100 grain weight (100GW) QTL on chromosome 5 were located in adjacent marker intervals. Four common QTL were detected across the RIL and F(2:3) generations, and two between the RIL and BC(2)F(2) generations. Each of five important mQTL (mQTL7-1, mQTL10-2, mQTL4-1, mQTL5-1 and mQTL1-3) included 7-12 QTL associated with 2-6 traits. In conclusion, we found evidence of strong influence of genetic structure and environment on QTL detection, high consistency of major QTL across environments and generations, and remarkable QTL co-location for grain yield components. Fine mapping for five major QTL (q100GW-1-1, q100GW-7-1, qGWP-4-1, qERN-4-1 and qKR-4-1) and construction of single chromosome segment lines for genetic regions of five mQTL merit further studies and could be put into use in marker-assisted breeding.