Transcriptome Analysis of Near-Isogenic Lines Provides Novel Insights into Genes Associated with Seed Low-Temperature Germination Ability in Maize (Zea mays L.)

Abstract

Maize originated from tropical regions and is extremely sensitive to low temperature during germination. Our previous work identified a major QTL, qp1ER1-1, for low temperature germination ability (LTGA) of maize. Here, we introgressed qp1ER1-1 from the tolerant line L220 into the sensitive line PH4CV to generate two near isogenic lines NIL220-3 and NIL220-25. When germinated under cold temperature for 25 days (Cold-25), the NILs showed similar seedling root length and shoot length to L220, but significantly higher than PH4CV. However, when germinated under cold temperature for 15 days (Cold-15) or under normal temperature (25 °C) for 3 days (CK-3), all lines showed similar seedling performance, indicating that introgression of qp1ER1-1 from L220 into PH4CV could improve LTGA of NIL220-3 and NIL220-25. The whole seedlings, including root and shoot, of Cold-15 and CK-3 were harvested for transcriptome analysis, when both stayed at a similar developmental stage. Dry seed embryo was sequenced as a non-germination control (CK-0). Compared with PH4CV, the tolerant line (L220, NIL220-3, and NIL220-25) specifically expressed genes (different expressed genes, DEGs) were identified for CK-0, Cold-15, and CK-3. Then, DEGs identified from Cold-15, but not from CK-0 or CK-3, were defined as tolerant line specifically expressed LTGA genes. Finally, 1786, 174, and 133 DEGs were identified as L220, NIL220-3, and NIL220-25 specifically expressed LTGA genes, respectively. Of them, 27 were common LTGA genes that could be identified from all three tolerant lines, with two (Zm00001d031209 and Zm00001d031292) locating in the confidence interval of qp1ER1-1. In addition, GO analysis revealed that L220 specifically expressed LTGA genes were majorly enriched in the cell division process and plasma membrane related categories. Taken together, these results provided new insight into the molecular mechanism of maize seed LTGA and facilitated the cloning of the qp1ER1-1 gene.

Understanding and Comprehensive Evaluation of Cold Resistance in the Seedlings of Multiple Maize Genotypes

“…Low temperature is among the major abiotic stresses that limited the productivity, quality, as well as distribution of maize [ 23 ]. Generally, tropical and subtropical maize are sensitive to cold stress [ 1 ]; therefore, maize that resists cold spells in early spring could broaden planting areas in high latitude regions, allow crop rotation, and increase yield by extending the growing season [ 24 ]. Moreover, the studies of different crops have shown that cold resistance is a complex biological process that involves interactions between agronomic traits and physiological processes and is dependent on the level of cold severity and timing in relation to the stage of crop development [ 7 , 25 , 26 , 27 ].…”

“…According to the results of previous studies [ 1 , 2 , 3 , 4 , 5 , 6 , 12 , 13 , 14 , 16 , 17 , 23 , 28 , 38 , 39 , 46 ] and our Pearson correlation and PCA analyses in the current study, distinct physiological processes and organ systems were involved in the onset, accumulation, and/or repair of maize cold injury; concomitantly, distinct molecular mechanisms were also likely involved in preventing (i.e., resistance) versus repairing cold injury (i.e., tolerance) by activating and inducing the expressions of some cold-responsive genes [ 47 ]. A diagram of hypothetical complex response mechanisms on cold resistance in maize was constructed ( Figure 6 ).…”

“…Maize ( Zea mays ), originating from tropical and subtropical regions, is extremely sensitive to cold stress, particularly at the seedling emergence stage [ 1 ]. Cold damage during maize seedlings development in early spring usually occurs at suboptimal temperatures of 10–15 °C or at even lower temperatures of 2–8 °C [ 2 ], which normally results in low seedling emergence/uniformity and biomass production, growth retardation, as well as occasionally irreversible tissue damage [ 3 , 4 , 5 ].…”

“…Cold damage during maize seedlings development in early spring usually occurs at suboptimal temperatures of 10–15 °C or at even lower temperatures of 2–8 °C [ 2 ], which normally results in low seedling emergence/uniformity and biomass production, growth retardation, as well as occasionally irreversible tissue damage [ 3 , 4 , 5 ]. The growth of cold-sensitive maize is limited in Northeast China, high–latitude areas since a transient chilling exposure, on average, every 3–4 years, may cause yield losses of 20% to 30% [ 1 , 6 ]. In agricultural practice, demand is high for the development of varieties with improved cold–resistance for the longer growing season, so that yield potentials can be fully realized in high–latitude cultivation regions.…”

Full-length transcriptome analysis of maize root tips reveals the molecular mechanism of cold stress during the seedling stage

“…In addition to genes related to the CBF cold response pathway, genes associated with signal transduction, membrane part, response stimulus, plant hormone signal transduction, abiotic stress response and zeatin biosynthesis, were significantly differentially expressed in plants under cold stress according to a comparison of transcriptomes between genotypes with contrasting levels of cold tolerance [9][10][11]. In maize, a number of cold response genes have been identified, and the functions of these genes were found to be largely similar to those of other plants [12][13][14][15][16][17][18][19][20]. Although thousands of cold-responsive genes have been identified in plants, most of these studies mainly used the Illumina sequencing platform, which generates short reads (< = 150 bp), making it difficult to quantify expression at the transcript level.…”