QTL mapping and transcriptome analysis identify candidate genes regulating pericarp thickness in sweet corn

BACKGROUND

In recent years, the planting area of sweet corn in China has expanded rapidly. Some new varieties with high yields and good adaptabilities have emerged. However, the improvement of edible quality traits, especially through the development of varieties with thin pericarp thickness, has not been achieved to date. Pericarp thickness is a complex trait that is the key factor determining the edible quality of sweet corn. Genetic mapping combined with transcriptome analysis was used to identify candidate genes controlling pericarp thickness.

RESULTS

To identify novel quantitative trait loci (QTLs) for pericarp thickness, a sweet corn BC₄F₃ population of 148 lines was developed using the two sweet corn lines M03 (recurrent parent) and M08 (donor parent). Additionally, a high-density genetic linkage map containing 3876 specific length amplified fragment (SLAF) tags was constructed and used for mapping QTLs for pericarp thickness. Interestingly, 14 QTLs for pericarp thickness were detected, and one stable QTL (qPT10-5) was detected across multiple years, which explained 7.78-35.38% of the phenotypic variation located on chromosome 10 (144,631,242-145,532,401). Forty-two candidate genes were found within the target region of qPT10-5. Moreover, of these 42 genes, five genes (GRMZM2G143402, GRMZM2G143389, GRMZM2G143352, GRMZM6G287947, and AC234202.1_FG004) were differentially expressed between the two parents, as revealed by transcriptome analysis. According to the gene annotation information, three genes might be considered candidates for pericarp thickness. GRMZM2G143352 and GRMZM2G143402 have been annotated as AUX/IAA transcription factor and ZIM transcription factor, respectively, while GRMZM2G143389 has been annotated as FATTY ACID EXPORT 2, chloroplastic.

CONCLUSIONS

This study identified a major QTL and candidate genes that could accelerate breeding for the thin pericarp thickness variety of sweet corn, and these results established the basis for map-based cloning and further functional research.

Bridging Sensory Evaluation and Consumer Research for Strategic Leafy Brassica (Brassica oleracea) Improvement

Plant breeders working with new or underrepresented horticultural crops often have minimal sensory resources available to aid in the breeding and selection of new varieties. Kale (Brassica oleracea var. acephala) is a recently popularized horticultural crop in Western markets, however, plant breeding programs have little knowledge regarding the underlying sensory characteristics motivating this trend. We employed a multilayered, sensory-driven approach to understand the inherent consumer values, sensory attributes, and consumer preferences for kale types currently available on the market and novel genotypes from the Cornell AgriTech vegetable breeding program. Underlying consumer values related to storability, health and wellbeing, and sensory characteristics were identified through Qualitative Multivariate Analysis (QMA). A trained descriptive panel developed a lexicon of 44 sensory attributes common within kale germplasm, 21 of which exhibited significant differences among the 15 tested kale genotypes. Following a consumer test, four clusters of kale consumers were identified with agglomerative hierarchical clustering (AHC) and external preference mapping was used to connect consumer hedonic scores with descriptive data. Consumers demonstrated a preference for familiar kale types (that is, curly types), while new test hybrids scored favorably within flavor and appearance modalities. Preference mapping highlighted the utility of plant breeding in developing products to expand the existing sensory space. This work provides important resources for horticultural crop selection efforts, and it serves as a strategic model for breeding programs working with new or unfamiliar traits. PRACTICAL APPLICATION: Plant breeders are responsible for selecting and improving traits that influence consumer acceptance, including quality traits such as appearance and flavor. Understanding the relative importance of sensory characteristics and the variation of these sensory characteristics can help plant breeders prioritize these traits within their program. We have developed a standardized sensory lexicon for kale and related leafy Brassicas, identified variation for texture and flavor in our breeding program, and gained a better understanding of consumer preferences to guide future breeding efforts.

Gene loci in maize influencing susceptibility to chilling dependent photoinhibition of photosynthesis

Variation in tolerance in chilling-dependent photoinhibition has been associated with a wide range of traits in comparative physiological studies. A sweet corn (Zea mays L.) population of 214 F(2:3 )families previously mapped to near-saturation with 93 RFLP DNA markers were subjected to low temperature and high-light events prior to measurement of the maximum dark-adapted quantum efficiency of PS II (F(v)/F(m)), to identify loci associated with variation in chilling-dependent photoinhibition. In the first assay with ten families varying in seedling growth and germination, significant differences were observed among families in their response to and recovery from exposure to high light at low temperature. All the 214 F(2:3) families from this population were then evaluated for tolerance of chilling-dependent photoinhibition in a controlled environment and then in three replicated trials in the field, each following naturally occurring chilling events during spring. The measured effects on F(v)/F(m) were analyzed with software that mapped segregating loci that regulate trait expression and linked to genetic markers (PLABQTL). QTL 3.096 (i.e. 96 cM on chromosome three) was consistently identified in both controlled environment and in the mean of the three field trails. Another QTL at 8.025, described the greatest percentage of total phenotypic variance (ca. 10%) for the mean reduction in F(v)/F(m) of all three periods of measurement in the field. A third QTL (4.136) showed a highly significant association in the third field trial. These three QTLs were closely associated with genes that have been mechanistically related to photoinhibition tolerance and repair. The results suggest that the ratio of F(v)/F(m) is an approach that may be used in establishing marker-assisted breeding for improved tolerance to chilling of maize in the light and in turn better early-season growth in cool temperate climates.

Current models for starch synthesis and the sugary enhancer1 (se1) mutation in Zea mays

Among the desirable quality traits essential for commercial production of fresh or processed sweet corn, kernel sugar content is universally important. In sweet corn genotypes the primary kernel sugar is sucrose, which is elevated at the expense of starch, particularly amylopectin. Sweet corn mutations have been traditionally divided into two classes. Generally speaking, class one mutations affect cytosolic reactions early in the process of starch synthesis, before starch is synthesized, and class two mutations affect reactions within the amyloplast directly involving starch granule assembly. Two widely used but previously unclassified mutations are sugary1 (su1) and sugary enhancer1 (se1). The se1 gene is a recessive modifier of su1; therefore, both genes require mutual discussion. This review provides current information about the su1 and se1 maize endosperm mutations and describes evidence further supporting previous suggestions that they fit criteria for categorization as class two mutants [Science 151 (1966) 341]. Information on the genetics and phenotype of se1 will be summarized and the hypothesized role of the se1 gene product discussed within the context of current models for starch synthesis in Zea mays L.

Quantification of carotenoid and tocopherol antioxidants in Zea mays

Recent investigations into carotenoid and tocopherol biological activity in mammalian systems indicate that these antioxidants are associated with the prevention of degenerative diseases. Both carotenoids and tocopherols can be found in corn kernel tissue. A replicated survey of 44 sweet and dent corn lines was conducted to determine qualitative and quantitative variability of lutein, zeaxanthin, beta-cryptoxanthin, alpha-carotene, and beta-carotene, as well as the alpha-, delta-, and gamma- forms of tocopherol. The primary carotenoids in fresh market sweet corn were found to be lutein and zeaxanthin, with the gamma form dominating among the tocopherols. Mean values among the genotypes were observed to range from 0 to 20.0 and 2.4 to 63.3 microg/g dry weight for lutein and gamma-tocopherol, respectively, indicating variability among genotypes in genes regulating the metabolism of these compounds. The observed genetic variability suggests profound differences in potential health promotion among genotypes and supports the feasibility of developing germplasm with enhanced levels of these antioxidant compounds at dosages that could promote health among the consuming public.