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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (4): 791-800.doi: 10.3724/SP.J.1006.2022.14062

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

Fine mapping of yellow-green leaf gene (ygl2) in soybean (Glycine max L.)

WANG Hao-Rang1(), ZHANG Yong2, YU Chun-Miao2, DONG Quan-Zhong, LI Wei-Wei1,3, HU Kai-Feng, ZHANG Ming-Ming2, XUE Hong, YANG Meng-Ping2, SONG Ji-Ling, WANG Lei2, YANG Xing-Yong, QIU Li-Juan2,*()   

  1. 1Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    2Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161606, Heilongjiang, China
    3College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
  • Received:2021-04-16 Accepted:2021-07-12 Online:2022-04-12 Published:2021-08-06
  • Contact: QIU Li-Juan E-mail:wanghaorang1018@163.com;qiulijuan@caas.cn
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    National Natural Science Foundation of China(31630056);Central Public-intreest Scientific Institution Basal Research Fund(S2021ZD02)

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Abstract:

Leaf is the main organ of photosynthetic carbon assimilation in soybean, and its color is not only related to the trapping power and conversion efficiency of light energy, but also closely related to the yield of soybean. Therefore, the mining of soybean leaf color-related genes is of great significance to analyze the yield of soybean from the pathway of photosynthetic carbon assimilation. Yellow-green leaf is a mutation type different from common green leaves of soybean, and it is an important genetic material to explore the genes related to leaf color of soybean. In this study, we found a yellow-green leaf mutant ygl2 (yellow-green leaf 2), which was naturally mutated from soybean strain GL11, and its yellow-green leaf phenotype could be stably inherited. Compared with the green leaf wild type GL11, the leaf chlorophyll content of mutant ygl2 decreased significantly, and there were significant differences in plant height, 100-grain weight, and protein content. The segregated population was constructed by GL11 and ygl2. Genetic analysis showed that the yellow-green leaf phenotype of ygl2 was controlled by a pair of recessive nuclear genes. The yellow-green leaf gene ygl2 was located between SSR markers 02_104 and 02_107 at the end of chromosome 2 using the isolated population, with an interval physical distance of 56.1 kb, and contained nine genes. These results laid a solid foundation for map-based cloning and molecular marker-assisted breeding of yellow and green leaf genes in soybean.

Key words: soybean, yellow-green leaf mutant, genetic analysis, fine mapping

Fig. 1

Phenotypes of ygl2 mutant and wild type GL11 A: seedling phenotype of mutant ygl2 and wild type GL11; B: leaf phenotype of mutant ygl2 and wild type GL11 at grain filling stage. Bar: 4 cm."

Fig. 2

Main agronomic traits of between ygl2 mutant and wild type GL11 Error bar indicates standard error (SE); * and ** indicate significant difference at the 0.05 and 0.01 probability levels, respectively."

Fig. 3

Photosynthetic pigment contents in leaves of ygl2 mutant and GL11 at seedling stage The content and ratio of photosynthetic pigments in the leaves of wild type GL11 and mutant ygl2 at the fourth trifoliolate stage (V4 stage). Error bar indicates standard error (SE); * and ** indicate significant difference at the 0.05 and 0.01 probability levels, respectively."

Table 1

Leaf color separation of hybrid F2 between mutant ygl2 and normal green variety"

组合名称
Combination		 总株数
Total number of plants		 绿叶植株数
No. of green leaf plants		 黄绿叶植株数
No. of yellow-green leaf plants		 期望比
Expected ratio		 卡方值
χ2 3:1		 P
ygl2×GL11 567 412 155 3:1 1.529 0.199

Fig. 4

Identification of candidate regions of yellow green leaf gene by ED association method The abscissa is the name of the chromosome, the colored dot represents the ED value of each SNP locus, the black line is the fitted ED value, and the red dotted line represents the significant correlation threshold."

Table 2

Molecular markers used for fine mapping"

引物名称
Primer name		 正向引物
Forward primer (5°-3°)		 反向引物
Reverse primer (5°-3°)
02_55 GTGTTCCACTCCACGTTTCC CATTTCCCCTTTCACAATCG
02_81 AACCGAGTTTGGTTCGATTC TGCTGCTTGATGATGAGGAC
02_90 CCATCTTATGGACTTGTTTGGA GCCAAGAATGACCATTATGC
02_101 TCACTAATCACAACAACCCAAA CGACCGGTGTGTTTAAGGTC
02_103 TCAGTCGCAGATTGATCAGG CCCAATTGTATCCATCAACG
02_104 AACCTAGCATTGCAACCTGC TCATCACCCCTTATCCGTTC
02_107 AAAACGAGGCCTTAATCGAAA AAACCAAAGAATACCGTGAAAAA
02_110 CGAAATGCCACCTTTTCAAT AGCAAACTAAGGTCGTTTTCG
02_117 GCAGTTGTGCGTGGGAGAGAG GCGACATAGCTAATTAAGTAAGTT
02_122 GCGTGGTGCACGATCATATAGA GCGTCTCCTTCGCTATCTCAAAC
02_125 CCAGGAATGCAGGTTTCTCT CGTGACTCTTCTTCCTTTCCA
02_130 AATGGAGAGGGGAACACAACT CCTAACGCACGAAATTTTCTC
ID2192 GCCTAATTTTGGCACCTTCA CACTCCTCTGCTTTGTTTGCT

Fig. 5

Fine mapping of ygl2 gene on chromosome 2 A: graphical genotypes of 6 recombinants (2001, 2006, 2027, 2144, CJ50, and 1054) carrying recombination events in the ygl2 region, and the genotypes of ygl2 for these recombinants were confirmed based on the phenotypic segregation pattern in their progenies; B: nine genes were identified within the delimited region of ygl2."

Table 3

Annotated genes and their putative functions in the target intervals"

基因名称
Gene name		 推测功能
Putative function
Glyma.02G304600 未知 Unknown
Glyma.02G304700 铁氧还蛋白氧化还原酶 Ferredoxin oxidoreductas
Glyma.02G304800 未知 Unknown
Glyma.02G304900 F-box相关 F-box-like
Glyma.02G305000 DNAj同源亚家族c成员 DNAj homolog subfamily c member
Glyma.02G305100 非特异性蛋白酪氨酸激酶/胞浆蛋白酪氨酸激酶/双特异性激酶
Non-specific protein-tyrosine kinase/cytoplasmic protein tyrosine kinase/dual-specificity kinase
Glyma.02G305200 核孔复合体蛋白Nup133 (NUP133) Nuclear pore complex protein Nup133 (NUP133)
Glyma.02G305300 钙转运ATP酶/钙转运p型 Calcium-transporting ATPase/calcium-translocating p-type
Glyma.02G305400 叶绿素a/b结合蛋白 Chlorophyll a/b binding protein

Fig. 6

Relative expression patterns of two candidate genes SAM: stem apical meristem. Error bar indicates standard error (SE); * and ** indicate significant difference at the 0.05 and 0.01 probability levels, respectively."

Fig. 7

Relative expression profiles of nine candidate genes Data are from Phytozome v12.1."

[1] Chen Z C, Wang L, Dai Y X, Wan X C, Liu S R. Phenology-dependent variation in the non-structural carbohydrates of broadleaf evergreen species plays an important role in determining tolerance to defoliation (or herbivory). Sci Rep, 2017, 7:10125-10135.
doi: 10.1038/s41598-017-00109-8
[2] Xiong L R, Du H, Zhang K Y, Lyu D, He H L, Pan J, Cai R, Wang G. A mutation in CsYL2.1 encoding a plastid isoform of triose phosphate isomerase leads to yellow leaf 2.1 (yl2.1) in cucumber (Cucumis sativus L.). Int J Mol Sci, 2020, 22:322-335.
doi: 10.3390/ijms22010322
[3] Wilson-Sanchez D, Rubio-Diaz S, Munoz-Viana R, Manuel Perez-Perez J, Jover-Gil S, Ponce M R, Micol J L. Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants. Plant J, 2014, 79:878-891.
doi: 10.1111/tpj.2014.79.issue-5
[4] Matsuda O, Tanaka A, Fujita T, Iba K. Hyperspectral imaging techniques for rapid identification of Arabidopsis mutants with altered leaf pigment status. Plant Cell Physiol, 2012, 53:1154-1170.
doi: 10.1093/pcp/pcs043 pmid: 22470059
[5] Fromme P, Melkozernov A, Jordan P, Krauss N. Structure and function of photosystem I: interaction with its soluble electron carriers and external antenna systems. FEBS Lett, 2003, 555:40-44.
pmid: 14630316
[6] Johnson M P. Correction: photosynthesis. Essays Biochem, 2016, 60:255-273.
doi: 10.1042/EBC20160016
[7] Sandhu D, Atkinson T, Noll A, Johnson C, Espinosa K, Boelter J, Abel S, Dhatt B K, Barta T, Singsaas E, Sepsenwol S, Goggi A S, Palmer R G. Soybean proteins GmTic110 and GmPsbP are crucial for chloroplast development and function. Plant Sci, 2016, 252:76-87.
doi: 10.1016/j.plantsci.2016.07.006
[8] Xia Y, Li Z, Wang J W, Li Y H, Ren Y, Du J J, Song Q L, Ma S C, Song Y L, Zhao H Y, Yang Z Q, Zhang G S, Niu N. Isolation and identification of a TaTDR-like wheat gene encoding a bHLH domain protein, which negatively regulates chlorophyll biosynthesis in Arabidopsis. Int J Mol Sci, 2020, 21:629-642.
doi: 10.3390/ijms21020629
[9] South P F, Cavanagh A P, Liu H W, Ort D R. Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field. Science, 2019, 363:45.
doi: 10.1126/science.aat9077
[10] Killough D T, Horlacher W R. The inheritance of virescent yellow and red plant colors in cotton. Genetics, 1933, 18:329-334.
doi: 10.1093/genetics/18.4.329 pmid: 17246695
[11] Granick S. Magnesium protoporphyrin as a precursor of chlorophyll in Chlorella. J Biol Chem, 1948, 175:333-342.
doi: 10.1016/S0021-9258(18)57262-8
[12] Brestic M, Zivcak M, Kunderlikova K, Allakhverdiev S I. High temperature specifically affects the photoprotective responses of chlorophyll b-deficient wheat mutant lines. Photosynt Res, 2016, 130:251-266.
doi: 10.1007/s11120-016-0249-7
[13] Wu Z M, Zhang X, Wang J L, Wan J M. Leaf chloroplast ultrastructure and photosynthetic properties of a chlorophyll-deficient mutant of rice. Photosynthetica, 2014, 52:217-222.
doi: 10.1007/s11099-014-0025-x
[14] Oh S A, Park J H, Lee G I, Paek K H, Park S K, Nam H G. Identification of three genetic loci controlling leaf senescence in Arabidopsis thaliana. Plant J, 1997, 12:527-535.
pmid: 9351240
[15] Zhang J Y, Sui C H, Liu H M, Chen J J, Han Z L, Yan Q, Liu S Y, Liu H Z. Effect of chlorophyll biosynthesis-related genes on the leaf color in Hosta (Hosta plantaginea Aschers) and tobacco(Nicotiana tabacum L.). BMC Plant Biol, 2021, 21:45.
doi: 10.1186/s12870-020-02805-6
[16] Robert A S, Brian M P, Maarten K, Peter H Q. Molecular analysis of the phytochrome deficiency in an aurea mutant of tomato. Mol Gene Genet Mgg, 1988, 213:9-14.
[17] Zhu Y, Yan P W, Dong S Q, Hu Z J, Wang Y, Yang J S, Xin X Y, Luo X J. Map-based cloning and characterization of YGL22, a new yellow-green leaf gene in rice (Oryza sativa). Crop Sci, 2021, 61:529-538.
doi: 10.1002/csc2.v61.1
[18] Zhang K J, Li Y, Zhu W W, Wei Y F, Njogu M, Lou Q F, Li J, Chen J F. Fine mapping and transcriptome analysis of virescent leaf gene v-2 in cucumber (Cucumis sativus L.). Front Plant Sci, 2020, 11:1458-1470.
[19] Qin D D, Dong J, Xu F C, Guo G G, Ge S T, Xu Q, Xu Y X, Li M F. Characterization and fine mapping of a novel barley stage green-revertible albino gene (HvSGRA) by bulked segregant analysis based on SSR assay and specific length amplified fragment sequencing. BMC Genomics, 2015, 16:838.
doi: 10.1186/s12864-015-2015-1
[20] Li T C, Yang H Y, Lu Y, Dong Q, Liu G H, Chen F, Zhou Y B. Comparative transcriptome analysis of differentially expressed genes related to the physiological changes of yellow-green leaf mutant of maize. PeerJ, 2021, 9:e10567.
[21] Liu M F, Wang Y Q, Nie Z X, Gai J Y, Bhat J A, Kong J J, Zhao T J. Double mutation of two homologous genes YL1 and YL2 results in a leaf yellowing phenotype in soybean [Glycine max (L.) Merr.]. Plant Mol Biol, 2020, 103:527-543.
doi: 10.1007/s11103-020-01008-9
[22] Sam R, Taylor A, Carly G, Katherine E, Sarah P, Alcira G, Reid P, Devinder S. Candidate gene identification for a lethal chlorophyll-deficient mutant in soybean. Agronomy, 2014, 4:462-469.
doi: 10.3390/agronomy4040462
[23] Campbell B W, Mani D, Curtin S J, Slattery R A, Michno J, Ort D R, Schaus P J, Palmer R G, Orf J H, Stupar R M. Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants. G3: Gen Genom Genet (Bethesda), 2014, 5:123-131.
[24] Kato K K, Palmer R G. Duplicate chlorophyll-deficient loci in soybean. Genome, 2004, 47:190-198.
pmid: 15060615
[25] Cai Z J, Steven R R, Richard M S. Regulation of photosynthesis in developing leaves of soybean chlorophyll-deficient mutants. Photosynth Res, 1997, 51:185-192.
doi: 10.1023/A:1005824706653
[26] Palmer R G, Nelson R L, Bernard R L, Stelly D M. Genetics and linkage of three chlorophyll-deficient mutants in soybean: y19, y22, and y23. J Hered, 1990, 81:404-406.
[27] Yu J S. Genetic studies with Shennong 2015, a lethal yellow mutant (y21) in soybean. Hereditas, 1986, 8:13-15.
[28] Wilcox J R, Probst A H. Inheritance of a chlorophyll-deficient character in soybeans. J Hered, 1969, 60:115-116.
doi: 10.1093/oxfordjournals.jhered.a107950
[29] Woodworth C M, Williams L F. Recent studies on the genetics of the soybeanl. Agron J, 1938, 30:125-129.
doi: 10.2134/agronj1938.00021962003000020006x
[30] Probst A H. The Inheritance of leaf abscission and other characters in soybeans1. Agron J, 1950, 42:35-45.
doi: 10.2134/agronj1950.00021962004200010007x
[31] Wang M, Li W Z, Fang C, Xu F, Liu Y C, Wang Z, Yang R, Zhang M, Liu S L, Lu S J, Lin T, Tang J Y, Wang Y Q, Wang H R, Lin H, Zhu B G, Chen M S, Kong F J, Liu B H, Zeng D L, Jackson S A, Chu C C, Tian Z X. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat Genet, 50:1435-1441.
[32] 邱丽娟. 大豆种质资源描述规范和数据标准. 北京. 中国农业出版社, 2006. p 22.
Qiu L J. Description and Data Standards for Soybean [Glycine max (L.) Merrill]. Beijing: China Agriculture Press, 2006. p22 (in Chinese).
[33] Song Q J, Jenkins J, Jia G F, Hyten D L, Pantalone V, Jackson S A, Schmutz J, Cregan P B. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. BMC Genomics, 2016, 17:33.
doi: 10.1186/s12864-015-2344-0
[34] Hill J T, Demarest B L, Bisgrove B W, Gorsi B, Su Y C, Yost H J. MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq. Genome Res, 2013, 23:687-697.
doi: 10.1101/gr.146936.112
[35] Song Q J, Jia G F, Zhu Y L, Grant D, Nelson R T, Hwang E Y, Cregan P B. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci, 2010, 50:1950-1960.
doi: 10.2135/cropsci2009.10.0607
[36] Richter A S, Banse C, Grimm B. The GluTR-binding protein is the heme-binding factor for feedback control of glutamyl-tRNA reductase. eLife, 2019, 8:e46300.
[37] Lee S, Kim J H, Yoo E S, Lee C H, Hirochika H, An G. Differential regulation of chlorophyll a oxygenase genes in rice. Plant Mol Biol, 2005, 57:805-818.
doi: 10.1007/s11103-005-2066-9
[38] Zhang H Y, Zhang D, Han S, Zhang X, Yu D Y. Identification and gene mapping of a soybean chlorophyll efficient mutant. Plant Breed, 2011, 130:133-138.
doi: 10.1111/pbr.2011.130.issue-2
[39] Eskins K, Banks D J. The relationship of accessory pigments to chlorophyll a content in chlorophyll-deficient peanut and soybean varieties. Photochem Photobiol, 2010, 30:585-588.
doi: 10.1111/php.1979.30.issue-5
[40] Palmer R G, Xu M. Positioning 3 qualitative trait loci on soybean molecular linkage group E. J Hered, 2008, 99:674-678.
doi: 10.1093/jhered/esn070 pmid: 18779225
[41] Terry M J, Ryberg M, Raitt C E, Page A M. Altered etioplast development in phytochrome chromophore-deficient mutants. Planta, 2001, 214:314-325.
pmid: 11800397
[42] Millar A J, Kay S A. Integration of circadian and phototransduction pathways in the network controlling CAB gene transcription in Arabidopsis. Proc Natl Acad Sci USA, 1997, 93:15491-15496.
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