Identification of Differentially Expressed Genes Involved in the Molecular Mechanism of Pericarp Elongation and Differences in Sucrose and Starch Accumulation between Vegetable and Grain Pea (Pisum sativum L.)
Abstract
:1. Introduction
2. Results
2.1. The Phenotypic Traits of Vegetable and Grain Pea Pericarp at Five Developmental Stages
2.2. RNA-seq of the Pea Pericarp Transcriptome
2.3. Analysis of the Expression Level and Differentially Expressed Genes (DEGs)
2.4. GO and KEGG Classification
2.5. DEGs Related to Pod Elongation
2.6. DEGs Related to Pod Sucrose Metabolism
2.7. DEGs Related to Pericarp Starch Synthesis
3. Discussion
4. Materials and Methods
4.1. Plant Material
4.2. Measurement of the Phenotypic Traits of the Two Cultivars
4.3. Illumina Sequencing and Mapping
4.4. Expression Level Analysis and Gene Annotation
4.5. qRT-PCR Validation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Transcriptome Sample | Total Clean Reads | Clean Bases (bp) | Q30 (%) | GC (%) | Total Mapped Reads (%) |
---|---|---|---|---|---|
WDZY-04_ I#1 | 50,177,200 | 7,327,792,349 | 96.765 | 43.575 | 44,475,396 (88.6%) |
WDZY-04_ I#2 | 49,061,332 | 7,188,004,754 | 96.825 | 43.245 | 43,387,875 (88.4%) |
WDZY-04_ I#3 | 50,406,494 | 7,306,478,571 | 96.675 | 43.37 | 44,730,739 (88.7%) |
WDZY-04_ II#1 | 52,539,172 | 7,662,278,764 | 96.74 | 43.3 | 46,613,759 (88.7%) |
WDZY-04_ II#2 | 43,217,524 | 6,246,391,018 | 96.585 | 43.475 | 38,215,715 (88.4%) |
WDZY-04_ II#3 | 64,372,148 | 9,362,931,919 | 96.835 | 43.36 | 57,145,999 (88.8%) |
WDZY-04_ III#1 | 70,119,664 | 10,202,409,573 | 96.815 | 43.245 | 62,179,404 (88.7%) |
WDZY-04_ III#2 | 42,849,086 | 6,201,019,405 | 96.655 | 43.22 | 37,836,945 (88.3%) |
WDZY-04_ III#3 | 50,627,610 | 7,391,282,480 | 97.485 | 43.045 | 45,179,447 (89.2%) |
WDZY-04_ IV#1 | 46,268,006 | 6,789,317,950 | 96.42 | 43.15 | 40,851,769 (88.3%) |
WDZY-04_ IV#2 | 55,534,482 | 8,050,533,372 | 96.705 | 43.16 | 49,204,948 (88.6%) |
WDZY-04_ IV#3 | 44,742,284 | 6,511,953,243 | 97.725 | 43.335 | 39,799,834 (89.0%) |
WDZY-04_ V#1 | 51,782,254 | 7,463,115,630 | 96.84 | 43.2 | 44,300,719 (85.6%) |
WDZY-04_ V#2 | 64,122,736 | 9,251,735,817 | 96.825 | 43.435 | 54,682,602 (85.3%) |
WDZY-04_ V#3 | 51,512,076 | 7,460,292,563 | 96.78 | 43.405 | 43,870,727 (85.2%) |
WDZY-14_ I#1 | 53,175,366 | 7,763,234,698 | 97.45 | 43.96 | 48,054,402 (90.4%) |
WDZY-14_ I#2 | 46,601,580 | 6,807,140,735 | 97.435 | 43.93 | 42,061,045 (90.3%) |
WDZY-14_ I#3 | 48,438,836 | 7,005,642,104 | 97.1 | 43.855 | 43,603,612 (90.0%) |
WDZY-14_ II#1 | 48,696,214 | 7,105,553,520 | 97.425 | 43.59 | 43,878,335 (90.1%) |
WDZY-14_ II#2 | 88,115,270 | 12,807,329,980 | 97.37 | 43.63 | 79,369,026 (90.1%) |
WDZY-14_ II#3 | 47,762,154 | 6,956,660,221 | 97.43 | 43.425 | 43,127,846 (90.3%) |
WDZY-14_ III#1 | 46,007,202 | 6,562,236,455 | 97.19 | 43.565 | 40,383,101 (87.8%) |
WDZY-14_ III#2 | 77,181,058 | 11,150,851,050 | 97.51 | 43.715 | 68,087,616 (88.2%) |
WDZY-14_ III#3 | 73,287,766 | 10,600,678,854 | 97.46 | 43.68 | 64,597,938 (88.1%) |
WDZY-14_ IV#1 | 46,437,750 | 6,721,682,138 | 96.93 | 43.925 | 41,388,924 (89.1%) |
WDZY-14_ IV#2 | 52,647,274 | 7,628,273,045 | 97.44 | 43.43 | 47,093,257 (89.5%) |
WDZY-14_ IV#3 | 56,984,532 | 8,236,432,557 | 96.845 | 43.255 | 50,542,076 (88.7%) |
WDZY-14_ V#1 | 58,306,756 | 8,466,331,576 | 97.485 | 44.04 | 46,961,785 (80.5%) |
WDZY-14_ V#2 | 45,359,128 | 6,567,548,081 | 97.49 | 44.155 | 36,311,644 (80.1%) |
WDZY-14_ V#3 | 65,632,458 | 9,522,635,831 | 97.47 | 44.01 | 52,782,939 (80.4%) |
Function | Gene_ID (NR database _id) | Growth Stage | WDZY -04#1 (FPKM) | WDZY -04#2 (FPKM) | WDZY -04#3 (FPKM) | WDZY -14#1 (FPKM) | WDZY -14#2 (FPKM) | WDZY -14#3 (FPKM) |
---|---|---|---|---|---|---|---|---|
SOD (superoxide dismutase) | XLOC_013249 (CAD42655.1) | Stage III | 0.84 | 0.92 | 1.48 | 0.32 | 0.19 | 0.19 |
XLOC_030516 (XP_013461079.1) | Stage V | 6.89 | 4.96 | 5.59 | 2.06 | 1.56 | 2.14 | |
XLOC_038705 (XP_004508271.1) | Stage V | 7.67 | 7.41 | 7.77 | 2.66 | 2.17 | 2.11 | |
POD (peroxidase) | XLOC_016611 (BAD97435.1) | Stage I | 12.48 | 14.26 | 7.99 | 0.67 | 0.77 | 0.52 |
XLOC_007148 (BAD97436.1) | Stage I | 156.02 | 161.58 | 124.67 | 51.6 | 55.49 | 54.04 | |
XLOC_034947 (BAD97436.1) | Stage I | 99.49 | 99.11 | 82.03 | 4.86 | 5.75 | 5.72 | |
XLOC_037479 (BAD97439.1) | Stage I | 38.62 | 37.61 | 37.81 | 10.94 | 12.67 | 15.38 | |
XLOC_031402 (CAA09881.1) | Stage I | 259.53 | 233.79 | 187.8 | 60.94 | 63.29 | 70.8 | |
XLOC_006267 (BAD97438.1) | Stage I | 44.78 | 41.83 | 36.77 | 14.98 | 15.67 | 15.38 | |
XLOC_006821 (BAD97436.1) | Stage I | 2.94 | 1.66 | 1.73 | 0 | 0.18 | 0 | |
XLOC_006267 (BAD97438.1) | Stage II | 14.48 | 14.26 | 13.78 | 5.87 | 6.66 | 6.89 | |
XLOC_016611 (BAD97435.1) | Stage II | 27.55 | 22.79 | 25.32 | 1.18 | 1.55 | 1.83 | |
XLOC_016611 (BAD97435.1) | Stage III | 26.89 | 28.71 | 30.24 | 2.3 | 2.01 | 1.81 | |
XLOC_018196 (XP_010104370.1) | Stage III | 0.28 | 0.07 | 0.32 | 0 | 0 | 0 | |
XLOC_007148 (BAD97436.1) | Stage III | 16.03 | 14.61 | 14.63 | 2.5 | 1.93 | 1.74 | |
XLOC_034947 (BAD97436.1) | Stage III | 1.18 | 1.42 | 1.45 | 0.38 | 0.09 | 0.15 | |
XLOC_031402 (CAA09881.1) | Stage III | 40.27 | 39.64 | 36.16 | 6.84 | 6.46 | 5.4 | |
XLOC_006267 (BAD97438.1) | Stage III | 27.95 | 26.15 | 25.67 | 7.26 | 5.53 | 5.6 | |
XLOC_016611 (BAD97435.1) | Stage IV | 26.56 | 24.06 | 21.55 | 0.91 | 0.69 | 0.74 | |
XLOC_034947 (BAD97436.1) | Stage IV | 0.27 | 0.16 | 0.16 | 2.38 | 3.29 | 3.73 | |
XLOC_037479 (BAD97439.1) | Stage IV | 0.43 | 1 | 0.48 | 1.61 | 1.62 | 1.81 | |
XLOC_031402 (CAA09881.1) | Stage IV | 0.62 | 0.99 | 0.89 | 2.57 | 2.7 | 4.32 | |
XLOC_007148 (BAD97436.1) | Stage V | 186.77 | 214.85 | 207.05 | 16.61 | 12.58 | 12.14 | |
peroxisome | XLOC_010379 (XP_013470503.1) | Stage I | 0.8 | 1.2 | 1.46 | 0.17 | 0.24 | 0.5 |
XLOC_010379 (XP_013470503.1) | Stage III | 1.48 | 1.55 | 1.92 | 0.33 | 0.47 | 0.51 | |
XLOC_010379 (XP_013470503.1) | Stage IV | 0.74 | 0.96 | 1.06 | 1.93 | 2.08 | 2.06 | |
XLOC_010379 (XP_013470503.1) | Stage V | 0.49 | 0.33 | 0.28 | 0.77 | 0.55 | 0.72 | |
ko(04146) | XLOC_019651 (GAU39672.1) | Stage I | 71.72 | 61.62 | 56.4 | 0 | 0 | 0 |
XLOC_019651 (GAU39672.1) | Stage II | 36.91 | 42.82 | 46.38 | 0 | 0 | 0 | |
XLOC_019651 (GAU39672.1) | Stage III | 50.38 | 54.52 | 25.55 | 0 | 0 | 0 | |
XLOC_019651 (GAU39672.1) | Stage IV | 27.28 | 15.42 | 23.63 | 0 | 0 | 0 | |
XLOC_019651 (GAU39672.1) | Stage V | 38.71 | 26.16 | 19.8 | 0 | 0 | 0 |
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Yang, P.; Li, Z.; Wu, C.; Luo, Y.; Li, J.; Wang, P.; Gao, X.; Gao, J.; Feng, B. Identification of Differentially Expressed Genes Involved in the Molecular Mechanism of Pericarp Elongation and Differences in Sucrose and Starch Accumulation between Vegetable and Grain Pea (Pisum sativum L.). Int. J. Mol. Sci. 2019, 20, 6135. https://doi.org/10.3390/ijms20246135
Yang P, Li Z, Wu C, Luo Y, Li J, Wang P, Gao X, Gao J, Feng B. Identification of Differentially Expressed Genes Involved in the Molecular Mechanism of Pericarp Elongation and Differences in Sucrose and Starch Accumulation between Vegetable and Grain Pea (Pisum sativum L.). International Journal of Molecular Sciences. 2019; 20(24):6135. https://doi.org/10.3390/ijms20246135
Chicago/Turabian StyleYang, Pu, Zhonghao Li, Caoyang Wu, Yan Luo, Jing Li, Pengke Wang, Xiaoli Gao, Jinfeng Gao, and Baili Feng. 2019. "Identification of Differentially Expressed Genes Involved in the Molecular Mechanism of Pericarp Elongation and Differences in Sucrose and Starch Accumulation between Vegetable and Grain Pea (Pisum sativum L.)" International Journal of Molecular Sciences 20, no. 24: 6135. https://doi.org/10.3390/ijms20246135