Fine mapping of the QTL cqSPDA2 for chlorophyll content in Brassica napus L

Identification of genetic loci and candidate genes regulating photosynthesis and leaf morphology through genome-wide association study in Brassica napus L

Rapeseed (Brassica napus L.) is a major agricultural crop with diverse applications, particularly in the production of seed oil for both culinary use and biodiesel. However, its photosynthetic efficiency, a pivotal determinant of yield, remains relatively low compared with other C3 plants such as rice and soybean, highlighting the necessity of identifying the genetic loci and genes regulating photosynthesis in rapeseed. In this study, we investigated 5 photosynthesis traits and 5 leaf morphology traits in a natural population of rapeseed, and conducted a genome-wide association study (GWAS) to identify significantly associated loci and genes. The results showed that the gas-exchange parameters of the dark reactions in photosynthesis exhibited a significant positive correlation with the chlorophyll content, whereas they showed a weaker negative correlation with the leaf area. By GWAS, a total of 538 quantitative trait nucleotides (QTNs) were identified as significantly associated with traits related to both leaf morphology and photosynthesis. These QTNs were classified into 84 QTL clusters, of which, 21 clusters exhibited remarkable stability across different traits and environmental conditions. In addition, a total of 3,129 potential candidate genes were identified to be significantly associated with the above-mentioned 10 traits, most of which were shared by certain traits, further indicating the reliability of the findings. By integrating GWAS data with GO enrichment analysis and gene expression analysis, we further identified 8 key candidate genes that are associated with the regulation of photosynthesis, chlorophyll content, leaf area, and leaf petiole angle. Taken together, this study identified key genetic loci and candidate genes with the potential to improve photosynthetic efficiency in rapeseed. These findings provide a theoretical framework for breeding new rapeseed varieties with enhanced photosynthetic capabilities.

Combo chloro-photosynthetic device and applications for greenhouse gas reduction campaign and smart agriculture

The increasing carbon dioxide (CO2) levels in the air pose a direct threat to all living organisms and the environment. Leveraging the ability of plants to absorb CO2 is one of the most effective methods for countering these rising CO2 levels. The present study aimes to develop a combo photosynthetic and chlorophyll-a sensor based on Non-Dispersive Infrared (NDIR) spectroscopy and an optical method. This sensor enables simultaneous, intensive measurement of net photosynthesis and chlorophyll-a content and yields accurate information. Comparative analysis of the efficacy of the sensors to that of a commercial instrument demonstrated that the measurement values obtained from the developed photosynthetic and chlorophyll-a sensors were not significantly different from those acquired with the commercial instrument (portable photosynthesis system LI-6400) and chlorophyll metre (SPAD-502), with a 95 % confidence level. Furthermore, the developed photosynthetic sensor could be used as a new correlation unit for chlorophyll-a content and net photosynthesis. Therefore, the sensor can be used to propose effective plantation processes to reduce atmospheric CO2 levels and in smart farming systems to control the quality of yields.

Genetic dissection of maize (Zea mays L.) chlorophyll content using multi-locus genome-wide association studies

BACKGROUND

The chlorophyll content (CC) is a key factor affecting maize photosynthetic efficiency and the final yield. However, its genetic basis remains unclear. The development of statistical methods has enabled researchers to design and apply various GWAS models, including MLM, MLMM, SUPER, FarmCPU, BLINK and 3VmrMLM. Comparative analysis of their results can lead to more effective mining of key genes.

RESULTS

The heritability of CC was 0.86. Six statistical models (MLM, BLINK, MLMM, FarmCPU, SUPER, and 3VmrMLM) and 1.25 million SNPs were used for the GWAS. A total of 140 quantitative trait nucleotides (QTNs) were detected, with 3VmrMLM and MLM detecting the most (118) and fewest (3) QTNs, respectively. The QTNs were associated with 481 genes and explained 0.29-10.28% of the phenotypic variation. Additionally, 10 co-located QTNs were detected by at least two different models or methods, three co-located QTNs were identified in at least two different environments, and six co-located QTNs were detected by different models or methods in different environments. Moreover, 69 candidate genes within or near these stable QTNs were screened based on the B73 (RefGen_v2) genome. GRMZM2G110408 (ZmCCS3) was identified by multiple models and in multiple environments. The functional characterization of this gene indicated the encoded protein likely contributes to chlorophyll biosynthesis. In addition, the CC differed significantly between the haplotypes of the significant QTN in this gene, and CC was higher for haplotype 1.

CONCLUSION

This study's results broaden our understanding of the genetic basis of CC, mining key genes related to CC and may be relevant for the ideotype-based breeding of new maize varieties with high photosynthetic efficiency.

Quantitative Trait Loci for Genotype and Genotype by Environment Interaction Effects for Seed Yield Plasticity to Terminal Water-Deficit Conditions in Canola (Brassica napus L.)

Canola plants suffer severe crop yield and oil content reductions when exposed to water-deficit conditions, especially during the reproductive stages of plant development. There is a pressing need to develop canola cultivars that can perform better under increased water-deficit conditions with changing weather patterns. In this study, we analysed genetic determinants for the main effects of quantitative trait loci (QTL), (Q), and the interaction effects of QTL and Environment (QE) underlying seed yield and related traits utilising 223 doubled haploid (DH) lines of canola in well-watered and water-deficit conditions under a rainout shelter. Moderate water-deficit at the pre-flowering stage reduced the seed yield to 40.8%. Multi-environmental QTL analysis revealed 23 genomic regions associated with days to flower (DTF), plant height (PH) and seed yield (SY) under well-watered and water-deficit conditions. Three seed yield QTL for main effects were identified on chromosomes A09, C03, and C09, while two were related to QE interactions on A02 and C09. Two QTL regions were co-localised to similar genomic regions for flowering time and seed yield (A09) and the second for plant height and chlorophyll content. The A09 QTL was co-located with a previously mapped QTL for carbon isotope discrimination (Δ¹³C) that showed a positive relationship with seed yield in the same population. Opposite allelic effects for plasticity in seed yield were identified due to QE interactions in response to water stress on chromosomes A02 and C09. Our results showed that QTL's allelic effects for DTF, PH, and SY and their correlation with Δ¹³C are stable across environments (field conditions, previous study) and contrasting water regimes (this study). The QTL and DH lines that showed high yield under well-watered and water-deficit conditions could be used to manipulate water-use efficiency for breeding improved canola cultivars.

Fine Mapping and Characterization of a Major Gene Responsible for Chlorophyll Biosynthesis in Brassica napus L

Rapeseed (Brassica napus L.) is mainly used for oil production and industrial purposes. A high photosynthetic efficiency is the premise of a high yield capable of meeting people’s various demands. Chlorophyll-deficient mutants are ideal materials for studying chlorophyll biosynthesis and photosynthesis. In a previous study, we obtained the mutant yl1 for leaf yellowing throughout the growth period by ethyl methanesulfonate mutagenesis of B. napus. A genetic analysis showed that the yl1 chlorophyll-deficient phenotype was controlled by one incompletely dominant gene, which was mapped on chromosome A03 by a quantitative trait loci sequencing analysis and designated as BnA03.Chd in this study. We constructed an F2 population containing 5256 individuals to clone BnA03.Chd. Finally, BnA03.Chd was fine-mapped to a 304.7 kb interval of the B. napus ‘ZS11’ genome containing 58 annotated genes. Functional annotation, transcriptome, and sequence variation analyses confirmed that BnaA03g0054400ZS, a homolog of AT5G13630, was the most likely candidate gene. BnaA03g0054400ZS encodes the H subunit of Mg-chelatase. A sequence analysis revealed a single-nucleotide polymorphism (SNP), causing an amino-acid substitution from glutamic acid to lysine (Glu1349Lys). In addition, the molecular marker BnaYL1 was developed based on the SNP of BnA03.Chd, which perfectly cosegregated with the chlorophyll-deficient phenotype in two different F2 populations. Our results provide insight into the molecular mechanism underlying chlorophyll synthesis in B. napus.

The Inheritable Characteristics of Monoecy and Parthenogenesis Provide A Means for Establishing A Doubled Haploid Population in the Economically Important Brown Alga Undaria pinnatifida (Laminariales, Alariaceae)

Monoecy and parthenogenesis exist in certain male and female gametophytes of the brown alga Undaria pinnatifida. The inheritance of these traits is not known. In this study, we made a cross between a male and a female gametophyte clone which could exhibit monoecy and parthenogenesis phenotypes, respectively, and obtained their next-generation gametophyte offspring. We found that under conditions suitable for gametogenesis, all of the male offspring (n = 100) exhibited monoecy phenotype and all of the female offspring (n = 100) only formed oogonia and underwent parthenogenesis, suggesting that monoecy and parthenogenesis phenotypes are inheritable. Then, we established a doubled haploid (DH) population through monoecious selfing and parthenogenesis, and evaluated the young sporophyte growth and the maximum quantum yield (Fv /Fm ) of 10 "male" and 10 "female" DH lines. On day 60, the average length of the "male" DH lines was significantly larger than that of the "female" DH lines, while their average Fv /Fm values were not significantly different. Monoecious selfing seemed superior to parthenogenesis as the sporophyte formation efficiency, and the young sporophyte growth was better in the former than in the latter. We also crossed two monoecious gametophytes with another male gametophyte, and a parentage analysis showed success of obtaining hybrid sporophytes, indicating that the female gametes released by the monoecious gametophyte can actually be fertilized by sperm. The approach of establishing a DH population proposed here will be useful in genetic breeding and quantitative trait loci mapping in U. pinnatifida and may be applicable to other kelp species.