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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (10): 2613-2620.doi: 10.3724/SP.J.1006.2023.33004

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

Map-based cloning and allelic analysis of gene controlling maize kernel mutant crk4

LI Meng-Yuan1(), ZHANG Wen-Cheng2, GAO Yong1, QIN Yong-Tian2, BO Shi-Rong1, SONG Kun-Yang1, TANG Ji-Hua1, FU Zhi-Yuan1()   

  1. 1National Key Laboratory of Wheat and Maize Crop Science / Collaborative Innovation Center of Henan Grain Crops / College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
    2Hebi Academy of Agricultural Sciences, Hebi 458030, Henan, China
  • Received:2023-01-14 Accepted:2023-04-17 Online:2023-10-12 Published:2023-04-24
  • Contact: E-mail: fuzhiyuan2004@163.com
  • Supported by:
    Key Technology Research and Development Program of Henan Province(232102111080)

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Abstract:

Kernel mutants are the important materials for cloning genes related to grain development and analyzing their genetic regulation mechanism. Crk4 (crumpled kernel 4) is a kernel mutant identified in the course of maize breeding and selection. Compared with the wild type, crk4 showed significantly lower in grain filling, grain weight, and germination rate. Genetic analysis showed that the mutant was controlled by a single recessive nuclear gene, which was mapped to a 614 kb physical distance on chromosome 5 by map-based cloning. In the 614 kb interval, 11 protein-coding genes were expressed in kernel. Sequence analysis revealed that there was a crk4-specific termination mutation in the second exon of Zm00001d017427 gene, which is caused by the deletion of C base. Zm00001d017427 encoded the metal-nicotianamine transporter (Sh4-shrunken4/Ysl2), which had been reported as the target gene of kernel mutant ysl2. The allelism test indicated that crk4 was a new allele mutant of ysl2/sh4. The identification of crk4 provided a new germplasm for elucidating the molecular regulation mechanism of Sh4 on seed development in maize.

Key words: maize, kernel mutant, crk4, map-based cloning, sh4/ysl2

Table 1

Primers for gene mapping"

引物名称
Primer name		 正向引物序列
Forward sequence (5'-3')		 反向引物序列
Reverse sequence (5'-3')
S09840
S09979		 ACGCCAGTGCTAATGGAATCG
ATCGCCCTTGAGGTGAAACAAC		 GCAACACAACACGCCAACAC
AGTCGAAAGCCAACCAAAGGAG
5-14 CATTTTGAGCGCTTTGATGA AGCAGCTCCTGTCGTGAAGT
5-32 GCCAGCGTCTTCTCTGATTC CTTGGTATGTTTCGCCAGGT
303 TCGGGTGGGATGGTTGGGGT GCCGTGGCGCTGAGAACAGT
499 ACTGCGACACTTGACGATGGGT GTGCCGGAGCAAACGAGCCT
5-38 GGTTGGGAGGATGATATCGA TCTCTCACTCTCAGGCAGCA
5-41 TGAGTCCGATGCTCACAGAG CTTTAGCGACGGCACTTACC
592-6 AAAAGCTTATACGGTTACAAGGT TGTTTACTGACATATGATCTCCAA
873-1 GGAAAGCGAAGCAGGTAA GTGGCTCAATCTGGAAACAT
5-284 CCCGAAGCTCGGTGCCAGGA GCAAGGACTTCAGTTGTTATGTTGCTC
S10043 GATTTCCTTGATCCTGGGTGAG TGTGTATGCAAATGGACTTAGC
S10049 TGGCATGGAGTCCACCAATTAC CACGGTGCCCAAACAAAAGAG
S10084 GGGTTGGGTTCAGGTGTTTCC GTCAGAGCACAAGGTGGGATG
S10118 AGAGCAGAGCGGAGCAGAC GTGTCAAGCAAAGCGTGTGTG

Fig. 1

Phenotypic analysis of crk4 A: segregation ears of Mo17×crk4 F3. The red arrows indicate crk4 kernels; bar: 1 cm. B: the comparison WT and crk4 kernels; bar: 1 cm. C: the comparison of kernel length, width, and thickness between WT and crk4. D: the comparison of 100-kernel weight between WT and crk4 with five replicates. E: the comparison of the longitudinal section between WT and crk4 kernels; bar: 1 cm. F: the comparison of the transverse section between WT and crk4 kernels; bar: 1 cm. G: the comparison of germination rate between WT and crk4. Values are represented as means ± SEs on histogram, *: P < 0.05; **: P < 0.01; ***: P < 0.001."

Table 2

Statistic analysis of kernels on F2 segregation ears"

果穗
Ear		 正常籽粒个数
No. of normal kernels		 突变籽粒个数
No. of mutant kernels		 籽粒总数
Total kernels		 实际比值
Observed ratio		 卡方值
χ2 test
374-1 329 116 445 2.84:1 0.270<χ20.05
374-2 271 85 356 3.19:1 0.240<χ20.05
374-3 296 98 394 3.02:1 0.003<χ20.05

Fig. 2

Map cloning of crk4 A: map-based cloning of crk4. The red number represents recombinants, and black number represents the population size. The crk4 is localized within a 614 kb interval on chromosome 5, containing 11 genes expressed in kernels. The target gene is indicated with red color. B: the schematic diagram of the structure of CRK4 gene. Black box represents exon, black line represents intron, red arrow indicates the mutation site in crk4, and black arrow indicates the mutation site in allelic mutants of ysl2 and sh4. C: the schematic diagram of the CRK4 protein with the conserved domains."

Table 3

Annotation of genes in the candidate intervals"

基因名称 Gene name 注释Annotation
Zm00001d017422 Homeobox-leucine zipper protein ATHB-6
Zm00001d017423 Origin recognition complex subunit 2
Zm00001d017424 ATP-dependent zinc metalloprotease FTSH 7 chloroplastic
Zm00001d017425 Cytochrome b5 (isoform A-like)
Zm00001d017427 Probable metal-nicotianamine transporter YSL16
Zm00001d017429 Yellow stripe 1
Zm00001d017432 Uncharacterized LOC100275088
Zm00001d017435 Uncharacterized LOC100275801
Zm00001d017438 Uncharacterized LOC100381739
Zm00001d017441 Cyclin-P4-1
Zm00001d017444 Probable WRKY transcription factor 51

Table 4

Primers for candidate genes"

引物名称
Primer name		 正向引物序列
Forward sequence (5'-3')		 反向引物序列
Reverse sequence (5'-3')
17427-1 TTGGCCAGAGAAAGCAACGA ATAAATGGCGGCGACCTCTC
17427-2 CAGGATTCCCCAGGAGAGGA CCAGGATTCGGGTGGATAGC
17427-3 ATGGATTCGGCTCTCATCGC CTCGCCAACGTGATGAAGGA
17427-4 CTTGGGTACGTCAGCTTGTA GGCGACTTTTGCTTCTACGTC
17432-1 ACTCCCTGCTCAGAAGCACT CCCAACTTCGTAGGCACGAT
17432-2 TTTGTAGCAAGACCAACAAGCAAAA TGTGCGAAATTGTGAATGACCA
17432-3 TCCAGACCATACGAGGTCAGT TGCTTCTGAGCAGGGAGTTT
17432-4 TGCCAGGTTTCAATGACCTCT CATTTGGCAGAATCCACGGC
17432-5 CGTCCACAGAGGGGACAAAC GCTCGGTGTCTTTTCAGGGA

Fig. 3

Allelic test of crk4 and ysl2 A: kernels on ysl2/+×crk4/+ hybrid ears, bar: 1 cm. B: kernels on crk4/+×ysl2/+ hybrid ears, bar: 1 cm. C: segregation statistics of kernels on ysl2/+×crk4/+ and crk4/+×ysl2/+ hybrid ears. D-E: mutation sequencing of Zm00001d017427 in mutant kernels from ears of double heterozygotes of crk4 and ysl2. D is for Zm00001d017427 in crk4 and E is for Zm00001d017427 in ysl2."

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