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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (12): 3120-3129.doi: 10.3724/SP.J.1006.2022.12077

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genetic analysis and gene mapping of the yellow midrib leaf mutant (yml) in rice (Oryza sativa L.)

GUO Jun-Yao1,2(), LIU Bin-Mei1,2, YANG Hui-Jie1,2, QIN Chao-Qi2, REN Yan2, JIANG Hong-Rui2, TAO Liang-Zhi2, YE Ya-Feng2, WU Yue-Jin1,2()   

  1. 1Institutes of Physical Science and Information Technology, Anhui University, Hefei 230031, Anhui, China
    2Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui, China
  • Received:2021-11-06 Accepted:2022-03-25 Online:2022-12-12 Published:2022-04-19
  • Contact: WU Yue-Jin E-mail:154519697@qq.com;yjwu@ipp.ac.cn
  • Supported by:
    Natural Science Foundation of Anhui Province(2108085MC99);Hefei Science and Technology Project(J2020G45);Anhui Science and Technology Major Project(202003c08020006)

Abstract:

Rice (Oryza sativa L.) is an important food crop, and its yield has been concerned for a long time. Rice leaves are the essential sites for photosynthesis, and leaf midrib is the tissue with the function of supporting and transporting. Meanwhile, the photosynthetic pigments present in leaf midrib can also provide a certain amount of photosynthesis. In this study, the yellow midrib leaf (yml) mutant obtained by the heavy ion beam implantation on indica rice 9311 was applied for genetic analysis and gene mapping. The mutant began to had the yellowing phenotype of leaf midrib about 5 days after flowering at heading stage, and the yellowing character was obvious at the late heading stage, and this change could last until the mature stage. At tillering stage, there was no significant difference in photosynthetic pigment content between the mutant and the wild type. However, compared with wild type at the late heading stage, the photosynthetic pigment content in the leaves and midribs of the mutant was significantly lower. Consequently, the photosynthetic efficiency of the mutant was substantially reduced, and the net photosynthetic rate was only 50.37% of wild type. At mature stage, plant height, panicle length, effective panicle, filled grain number per panicle, seed setting rate, and the 1000-grain weight of mutants were significantly lower than wild type. Genetic analysis revealed that this mutant character was controlled by a pair of recessive genes. By using map-based cloning technique, this gene was located on chromosome 6. Moreover, the gene was further located between InDel5 and RM3431 with a physical distance of approximately 700 kb by using simple repeat sequence (SSR) and insertional deletion (InDel) markers. This study provides a research basis for the subsequent cloning and functional analyses of the mutant gene.

Key words: Oryza sativa L., midrib, yellow, photosynthetic, gene mapping

Fig. 1

Phenotypic characteristics of wild type (9311) and mutant yml A: plants of wild-type (9311) and yml mutant at heading stage; Bar: 10 cm; B: flag leaf of wild-type (9311) and yml mutant at heading stage; Bar: 5 cm; C: panicle of wild-type (9311) and yml mutant; Bar: 5 cm."

Table 1

Agronomic traits of wild type (9311) and mutant yml"

材料
Material name
株高
Plant height
(cm)
穗长
Panicle length
(cm)
有效穗数
Effective
panicle
每穗实粒数
Filled grain number
per panicle
结实率
Seed setting rate (%)
千粒重
1000-grain weight (g)
9311 127.33±4.29 22.42±2.17 9.67±1.53 158.62±27.98 71.16±9.55 28.06±2.16
yml 97.41±4.15** 20.67±2.79* 4.67±0.58** 105.00±30.58** 43.20±9.02** 23.10±0.41**

Fig. 2

Contents and ratios of various photosynthetic pigments in leaves and midrib of wild type (9311) and mutant yml at different stages A: the content of various photosynthetic pigments in leaves of wild type (9311) and mutant yml at tillering stage; B: the content of various photosynthetic pigments in midrib of wild type (9311) and mutant yml at tillering stage; C: the content of various photosynthetic pigments in leaves of wild type (9311) and mutant yml at heading stage; D: the content of various photosynthetic pigments in midrib of wild type (9311) and mutant yml at heading stage; E: the ratio of carotenoids to total chlorophyll in leaves of wild type (9311) and mutant yml at tillering stage; F: the ratio of carotenoids to total chlorophyll in midrib of wild type (9311) and mutant yml at heading stage. *: P < 0.05; **: P < 0.01."

Table 2

Photosynthetic characteristics of wild type (9311) and mutant yml"

材料
Material
净光合速率
Photosynthetic rate
(μmol CO2 m-2 s-1)
蒸腾速率
Transpiration rate
(mol H2O m-2 s-1)
气孔导度
Stomatal conductance
(mmol H2O m-2 s-1)
胞间二氧化碳浓度
Intercellular CO2 concentration
(μmol CO2 L-1)
9311 14.95 ±0.74 3.96±0.33 279.97±3.72 338.00±7.21
yml 7.53±0.15** 5.96±0.34** 227.47±15.88** 390.00±9.54**

Fig. 3

Electrophoresis diagram of initial location of yml genes M: 9311; W: japonica var. Nipponbare; M: DL2000 marker."

Fig. 4

Linkage map of yml genes on chromosome 6 in rice"

Table 3

New developed polymorphic InDel makers based on the genome sequence differences between indica var. 9311 and japonica var. Nipponbare"

引物名称
Prime name
引物序列
Prime sequence
(5'-3')
物理位置
Physical position
(bp)
9311 PCR
产物大小
PCR product size of 9311
(bp)
日本晴PCR
产物大小
PCR product size of Nipponbare
(bp)
中花11 PCR
产物大小
PCR product size of Zhonghua 11 (bp)
InDel 3 F: CTGGCGGTCGAATTTCTTTA
R: GGCAAATTTCAGCCACAGAT
7,245,119-7,245,342 160 124 124
InDel 5 F: CAATCAGAATCTGCTTGCCA
R: ACACACATGGCAGGTCACAT
8,059,757-8,059,997 255 241 241
InDel 13 F: CAGCCACACATTTGGAACCA
R: CTGCAAAGGATCTTGATCCG
7,813,844-7,814,076 206 233 233

Table 4

Related genes and their putative functions in the target regions"

基因名称
Gene name
推测功能
Putative function
LOC_Os06g14420 Hydrolase, NUDIX family, domain containing protein, expressed
LOC_Os06g14650 Zinc finger, C3HC4 type domain containing protein, expressed
LOC_Os06g14670 ODORANT1, putative, expressed
LOC_Os06g14700 Myb-like DNA-binding domain containing protein, expressed
LOC_Os06g14710 Myb-like DNA-binding domain containing protein, expressed
LOC_Os06g14750 Phosphatidylinositol-4-phosphate 5-kinase family protein, putative, expressed
LOC_Os06g15380 Acylphosphatase, putative, expressed
LOC_Os06g15390 Acylphosphatase, putative, expressed
LOC_Os06g15410 Angel, putative, expressed
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