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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (3): 622-633.doi: 10.3724/SP.J.1006.2023.23024

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

QTL locating and genomic selection for tassel-related traits using F2:3 lineage haploids

XU Jia-Bo(), WU Peng-Hao, HUANG Bo-Wen, CHEN Zhan-Hui, MA Yue-Hong, REN Jiao-Jiao()   

  1. College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
  • Received:2022-03-03 Accepted:2022-06-07 Online:2023-03-12 Published:2022-07-07
  • Contact: REN Jiao-Jiao E-mail:1142019044@qq.com;renjiaojiao789@sina.com
  • Supported by:
    National Natural Science Foundation of China(U2003304);National Natural Science Foundation of China(32060484);National Natural Science Foundation of China(32001561);Scientific and Technological Talent Training Project for Excellent Youth in Tianshan Mountain of Autonomous Region(2018Q019);Natural Science Foundation of Xinjiang(2019D01A41);Postdoctoral Project(2018M643774);Xinjiang Main Crop Biological Breeding Innovation Project (I)—Maize Biological Breeding Innovation Project(2021A02001-2);Xinjiang Maize Green High Yield, Quality and Efficiency Technology Optimization Integration and Application Funding(2021B02002-2)

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Abstract:

Tassel size affects the nutrient allocation synthesized by photosynthesis in maize, which in turn affects ears development and the yield components, such as kernel rows, kernel number per row, seeding rate, and kernels weight per one hundred. In this study, haploids were induced using the F2:3 families, which were constructed from the elite inbred lines Zheng 58 and B73. Genotypes were obtained by 48K liquid phase hybridization capture probes technique, and phenotypes were evaluated in multi-environment trails. QTL mapping was performed using the inclusive composite interval mapping (ICIM) method. The RRBLUP model was used for genomic selection to explore the effects of training population size and the number of SNP markers on prediction accuracy. The results showed that the heritabilities of tassel length, tassel primary branch number, tassel secondary branch number, and tassel branch number were 0.82, 0.88, 0.84, and 0.88, respectively. Two QTL, located in bins 1.03 and 4.09, were detected for tassel length with phenotypic variation explained (PVE) of 6.02% and 11.10%, respectively. Two QTL, located in bins 1.05 and 4.05, were detected for tassel primary branch with PVE of 9.17% and 11.75%, respectively. Two QTL, located in bins 2.03 and 3.06, were detected for the tassel secondary branch with PVE of 5.51% and 5.65%, respectively. Two QTLs, located in bins 1.04 and 4.05, were detected for the tassel branch number with PVE of 9.37% and 10.83%, respectively. Tassel primary branch number and tassel branch number identified a same QTL located in bin 4.05 with multiple effects. The prediction accuracy of five-fold cross-validation for genomic selection was 0.36, 0.41, 0.28, and 0.37, respectively. When the training population reached 60% of the total population and the marker density reached 500, a high prediction accuracy could be obtained.

Key words: maize (Zea mays L.), haploid, tassel, QTLs, genomic selection

Table 1

Assessment of tassel related traits in maize haploids"

性状
Trait		 测定方法
Assessment
雄穗主轴长
Tassel length		 测量雄穗最底部分枝的基部至雄穗顶端的长度[17-18]。
Measure the length from the base of the lowest branch of the tassel to the tip of the tassel[17-18].
雄穗一级分枝数
Tassel primary branch number		 对基部与雄穗主茎直接相连的分枝进行计数[7]。
The branches whose base is directly connected to the main stem of the tassel were counted[7].
雄穗二级分枝数
Tassel secondary branch number		 对基部与一级分枝直接相连的分枝进行计数。
Counting of branches whose base is directly connected to the primary branches.
雄穗总分枝数
Tassel branch number		 计算雄穗一级分枝和雄穗二级分枝的总和[11,17]。
Calculate the sum of the tassel primary branche number and the tassel secondary branche number[11,17].

Table 2

Descriptive statistics of tassel related traits in maize haploids"

性状
Trait		 均值
Mean		 最小值
Min.		 最大值
Max.		 偏度
Skewness		 峰度
Kurtosis		 变异系数
CV
雄穗主轴长Tassel length (cm) 18.52 17.33 19.90 0.12 -0.57 0.03
雄穗一级分枝数Tassel primary branch number 5.85 3.79 8.32 0.16 -0.22 0.14
雄穗二级分枝数Tassel secondary branch number 0.79 0.50 1.23 0.48 -0.14 0.19
雄穗总分枝数Tassel branch number 6.64 4.33 9.51 0.17 -0.22 0.15

Table 3

Variance analysis and broad-sense heritability (H2) analysis for tassel traits in maize haploids"

性状
Trait		 方差来源
Source of variances		 自由度
DF		 均方
Mean of square		 F值
F-value		 P 值
P-value		 遗传力
H2
雄穗主轴长
Tassel length		 基因型Genotype (G) 199 5.27 2.56 <0.01** 0.82
环境Environment (E) 2 8.04 3.90 0.02*
基因×环境型
Genotype × environment (G×E)		 304 2.38 1.16 0.08
残差Error 506 2.06
雄穗一级分枝数
Tassel primary branch number		 基因型G 199 7.48 4.35 <0.01** 0.88
环境E 2 72.74 42.29 <0.01**
基因×环境型G×E 304 2.22 1.29 <0.01**
残差Error 506 1.72
雄穗二级分枝数
Tassel secondary branch number		 基因型G 199 0.35 2.67 <0.01** 0.84
环境E 2 6.71 51.14 <0.01**
基因×环境型G×E 304 0.14 1.06 0.28
残差Error 506 0.13
雄穗总分枝数
Tassel branch number		 基因型G 199 9.72 4.21 <0.01** 0.88
环境E 2 120.89 52.42 <0.01**
基因×环境型G×E 304 2.83 1.23 0.02*
残差Error 506 2.31

Fig. 1

Correlation analysis of tassel related traits in maize haploid *: P < 0.05; **: P < 0.01; ***: P < 0.001. The circle from small to large represents the correlation coefficient from low to high."

Fig. 2

QTLs mapping of tassel related traits in maize haploid population"

Table 4

QTL mapping of haploid tassel related traits under three environmental conditions"

性状
Trait		 QTL 染色体/bin
Chr./bin		 遗传位置
Genetic position (cM)		 物理距离a
Physical position (Mb)a		 LOD值
LOD-value		 表型贡献率
PVE (%)		 加性效应
Additive		 显性效应
Dominant		 基因效应b
Gene actionb		 参考文献
Reference
雄穗主轴长
Tassel length		 qTL1-1 1/1.03 34 32.50-32.53 3.01 6.02 0.05 −0.25 OD 贾波等[24] Jia B, et al.[24]
qTL4-1 4/4.09 69 223.30-224.37 5.40 11.10 0.27 −0.04 A
雄穗一级分枝数
Tassel primary branch number		 qTPBN1-1 1/1.05 61 102.35-105.19 4.98 9.17 0.37 −0.20 PD 杨钊钊等[6] Yang Z Z, et al.[6]
qTPBN4-1 4/4.05 31 75.57-79.81 6.29 11.75 −0.42 0.20 PD
雄穗二级分枝数
Tassel secondary branch number		 qTSBN2-1 2/2.03 35 26.29-27.50 2.69 5.51 −0.06 −0.01 A
qTSBN3-1 3/3.06 47 185.21-185.33 2.78 5.65 0.06 0.01 A 张先创[8] Zhang X C[8]
雄穗总分枝数
Tassel branch number		 qTBN1-1 1/1.04 46 56.92-57.40 5.11 9.37 0.42 −0.28 PD 张先创[8]、Upadyayula等[25]
Zhang X C[8]; Upadyayula, et al.[25]
qTBN4-1 4/4.05 31 75.57-79.81 5.80 10.83 −0.46 0.22 PD

Fig. 3

Genomic selection accuracy of tassel related traits in the haploid population"

Fig. 4

Genomic selection accuracy of tassel related traits in the haploid population with different training population sizes A: tassel length; B: tassel primary branch number; C: tassel secondary branch number; D: tassel branch number."

Fig. 5

Genomic selection accuracy of tassel related traits in the haploid population with different number of SNPs A: tassel length; B: tassel primary branch number; C: tassel secondary branch number; D: tassel branch number."

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