Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (20): 3931-3945.doi: 10.3864/j.issn.0578-1752.2023.20.002


QTL Analysis for Seeding Traits Related to Low Nitrogen Tolerance in Foxtail Millet

QIN Na(), FU SenJie, ZHU CanCan, DAI ShuTao, SONG YingHui, WEI Xin, WANG ChunYi, YE ZhenYan, LI JunXia()   

  1. Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002
  • Received:2023-03-23 Accepted:2023-05-30 Online:2023-10-16 Published:2023-10-31
  • Contact: LI JunXia


【Objective】The analysis of quantitative trait loci (QTL) related to low nitrogen tolerance traits of millet (Setaria italica L.) laid a foundation for fine mapping, cloning and functional research of low nitrogen tolerance genes. At the same time, it also provided technical support for revealing the genetic mechanism of low nitrogen tolerance of millet and breeding low nitrogen tolerance varieties. 【Method】The recombinant inbred line (RIL) population consisting of 120 family lines was used as experimental materials, that was constructed from parents Yugu 28, a low nitrogen tolerant variety, and Qiyehuang, a low nitrogen sensitive variety. The RIL populations were treated with low nitrogen and normal nitrogen at seedling stage, and seven traits were analyzed of hydroponic for 21 days, which inculding seedling length, maximum root length, root dry weight, seedling dry weight, plant dry weight, relative chlorophyll content and plant nitrogen content. At the same time, we used composite interval mapping (CIM) to locate and analyze QTLs for traits related to low nitrogen tolerance, and predicted the candidate genes in the confidence intervals of QTLS. 【Result】The traits associated with low nitrogen tolerance of RIL populations exhibited continuous distribution with apparent transgressive segregation both under low nitrogen and normal nitrogen levels, which conformed to the typical genetic characteristics of quantitative traits and were suitable for QTL genetic analysis. Correlation analysis showed that seeding length was positively correlated with maximum root length, root dry weight, seeding dry weight, plant dry weight and relative chlorophyll content, and maximum root length was negatively correlated with plant nitrogen content. A total of thirty-four QTLs related to seeding length, maximum root length, root dry weight, seeding dry weight, plant dry weight, relative chlorophyll content and plant nitrogen content were located under low nitrogen and normal nitrogen levels, which distributed on chromosomes from 1 to 9. They explained individually 5.15%-52.42% phenotypic variation. Ten QTLs were simultaneously detected under both two nitrogen levels, eleven and thirteen QTLs were only identified under single low nitrogen and normal nitrogen conditions, respectively. A total of fifteen QTLs were major QTL, and five major QTLs were repeatedly detected under both two nitrogen levels, which including qRDW3, qMRL1.1, qMRL1.2, qSL5 and qSPAD1. Five QTL overlaps were detected with gathering multiple QTLs under two nitrogen levels. Six candidate genes related to nitrogen metabolism were identified from the confidence interval of the five QTL overlaps, suggesting that genes related to nitrogen assimilation, absorption and utilization probably control the expression of these genes. 【Conclusion】Thirty-four QTLs were scattered on sixteen clusters of nine chromosomes. Based on gene annotation, a total of 6 candidate genes related to nitrogen metabolism were screened in foxtail millet, indicating the different traits involved in common genetic mechanisms, and the favorable alleles for low nitrogen tolerance can be polymerized by marker-assisted selection.

Key words: foxtail millet, recombinant inbred line (RIL), low nitrogen tolerance, QTL

Fig. 1

Phenotypic of recombinant inbred lines for sensitive to low nitrogen after hydroponic 21 d under low nitrogen (left) and normal nitrogen (right) conditions"

Table 1

Phenotypic analysis of the RIL population and its parents under normal (+N) and low (-N) nitrogen levels"

N level
亲本Parents t测验
t test
RIL群体RIL population
豫谷28 Yugu 28 七叶黄Qiyehuang 均值Mean 变异范围Range
SL (cm)
+N 29.10±1.60 24.40±0.90 * 27.90±1.10 15.20—39.50
-N 21.10±0.90 17.50±0.60 * 20.40±1.01 8.00—31.00
差异Difference (%) -27.50* -28.30* -26.88*
MRL (cm)
+N 16.10±1.10 11.20±0.70 ns 17.20±0.40 6.50—35.50
-N 18.10±0.30 14.20±0.40 * 22.50±1.10 8.20—40.50
差异Difference (%) 12.50* 17.86* 30.81**
RDW (g)
+N 0.040±0.0010 0.030±0.0010 * 0.030±0.010 0.010—0.050
-N 0.030±0.0020 0.020±0.0010 ns 0.020±0.0020 0.0010—0.040
差异Difference (%) -25.00* -33.30 ns -33.33**
SDW (g)
+N 0.10 ±0.020 0.060±0.0010 * 0.080±0.0020 0.040—0.160
-N 0.060±0.0020 0.010±0.0010 * 0.040±0.0010 0.010—0.10
差异Difference (%) -40.00** -83.30** -50.00**
PDW (g)
+N 0.15±0.030 0.080±0.0020 * 0.11±0.010 0.040—0.22
-N 0.080 ±0.0020 0.040±0.0010 * 0.060±0.0020 0.010—0.12
差异Difference (%) -46.67* -50.00* -45.45**
+N 31.70±1.90 25.20±2.01 * 31.30±2.20 23.05—36.57
-N 28.50±2.10 21.20±0.80 * 22.50±1.90 16.75—28.13
差异Difference (%) -10.10 ns -15.87* -28.11*
PNC (mg·100 mg-1)
+N 2.60±0.10 2.20±0.090 ns 2.70±0.10 1.89—4.82
-N 2.20±0.080 1.60±0.10 * 1.90±0.30 1.21—2.97
差异Difference (%) -15.38 ns -27.27* -29.63*

Fig. 2

Frequency distributionof the RIL population and its parents under normal (+N) and low (-N) nitrogen levels"

Table 2

Correlation among these seedling traits under -N and +N conditions"

N level
低氮-N 苗长SL 0.653** 0.584* 0.814** 0.798** 0.692** 0.142
主根长MRL 0.701** 0.568* 0.684** 0.583* -0.223*
根干质量RDW 0.646** 0.708** 0.561* 0.285*
苗干质量SDW 0.825** 0.675** 0.305*
总干质量PDW 0.794** 0.313*
叶绿素相对含量SPAD 0.724**
正常氮+N 苗长SL 0.795** 0.817** 0.792** 0.884** 0.830** 0.751** 0.256*
主根长MRL 0.806** 0.726** 0.806** 0.784** 0.696** -0.348**
根干质量RDW 0.652** 0.734** 0.805** 0.265* 0.217*
苗干质量SDW 0.633** 0.794** 0.852** 0.324*
总干质量PDW 0.749** 0.631** 0.352*
叶绿素相对含量SPAD 0.760** 0.554*
植株含氮量PNC 0.670**

Table 3

QTLs mapping for traits related to nitrogen tolerance"

N level
Marker interval
LOD value
Additive effect
Proportion of the variance explained (%)
低氮-N 1 qSL1 SICAAS1060—SICAAS1057 3.20 -0.88 5.15
3 qSL3 SICAAS3043—SICAAS3048 4.70 -1.71 20.39
5 qSL5 SICAAS5085—SICAAS5049 2.99 1.22 10.37
6 qSL6 SICAAS6055—SICAAS6008 3.30 1.13 8.72
7 qSL7 SICAAS7028—SICAAS7038 3.56 1.08 8.08
正常氮+N 3 qSL3.1 SICAAS3022—SICAAS3029 3.59 1.11 7.14
3 qSL3.2 SICAAS3029—SICAAS3034 3.37 1.15 7.51
5 qSL5.1 SICAAS5085—SICAAS5049 3.27 1.16 7.92
5 qSL5.2 SICAAS5055—SICAAS5083 3.49 -1.14 8.62
5 qSL5.3 SICAAS5083—SICAAS5034 3.49 -1.02 6.82
6 qSL6 SICAAS6019—SICAAS6005 2.99 -0.97 5.79
低氮-N 1 qMRL1.1 SICAAS1034—SICAAS1039 2.52 -2.82 27.31
1 qMRL1.2 SICAAS1039—SICAAS1008 4.72 -2.23 13.76
1 qMRL1.3 SICAAS1008—SICAAS1010 3.64 1.32 6.00
3 qMRL3 SICAAS3043—SICAAS3048 3.18 1.40 6.78
5 qMRL5.1 SICAAS5083—SICAAS5034 2.42 1.27 5.19
5 qMRL5.2 SICAAS5034—SICAAS5035 4.31 1.88 11.07
7 qMRL7 SICAAS7005—SICAAS7028 3.55 1.71 9.82
9 qMRL9 SICAAS9033—SICAAS9130 3.60 -1.74 8.31
正常氮+N 1 qMRL1.1 SICAAS1034—SICAAS1039 5.80 -2.44 28.50
1 qMRL1.2 SICAAS1039—SICAAS1008 7.35 -2.48 26.56
2 qMRL2 SICAAS2046—SICAAS2016 2.82 1.09 5.64
6 qMRL6 SICAAS6005—SICAAS6058 2.28 -1.18 6.56
8 qMRL8 SICAAS8001—SICAAS8007 3.39 -1.36 8.65
低氮-N 3 qRDW3 SICAAS3043—SICAAS3048 7.51 -0.36 28.54
6 qRDW6 SICAAS6055—SICAAS6008 2.23 0.19 6.86
7 qRDW7 SICAAS7005—SICAAS7028 2.30 -0.22 9.06
正常氮+N 1 qRDW1 SICAAS1057—SICAAS1052 2.95 -0.2 5.58
3 qRDW3.1 SICAAS3069—SICAAS3022 3.19 -0.26 8.59
3 qRDW3.2 SICAAS3022—SICAAS3029 4.32 -0.33 13.40
3 qRDW3.3 SICAAS3043—SICAAS3048 4.13 -0.34 14.62
4 qRDW4.1 SICAAS4060—SICAAS4033 2.20 0.26 9.04
4 qRDW4.2 SICAAS4003—SICAAS4062 3.45 0.38 17.53
9 qRDW9 SICAAS9024—SICAAS9027 2.02 0.28 7.89
低氮-N 1 qSDW1.1 SICAAS1060—SICAAS1057 2.76 -0.50 8.71
1 qSDW1.2 SICAAS1057—SICAAS1052 2.25 -0.41 5.69
3 qSDW3 SICAAS3043—SICAAS3048 5.43 0.78 23.00
正常氮+N 5 qSDW5.1 SICAAS5083—SICAAS5034 3.17 0.78 10.71
5 qSDW5.2 SICAAS5035—SICAAS5036 2.20 0.61 5.39
6 qSDW6.1 SICAAS6055—SICAAS6008 2.60 -0.63 6.86
6 qSDW6.2 SICAAS6008—SICAAS6081 2.81 -0.79 10.24
低氮-N 1 qPDW1.1 SICAAS1060—SICAAS1057 3.64 -0.92 15.67
1 qPDW1.2 SICAAS1057—SICAAS1052 2.28 -0.68 8.64
2 qPDW2 SICAAS2010—SICAAS2068 2.78 0.97 17.74
3 qPDW3 SICAAS3043—SICAAS3048 6.88 1.7 52.42
5 qPDW5 SICAAS5036—SICAAS5037 3.64 0.90 15.01
7 qPDW7 SICAAS7005—SICAAS7028 2.04 -0.59 6.28
正常氮+N 3 qPDW3 SICAAS3029—SICAAS3034 2.26 1.20 10.25
低氮-N 1 qSPAD1 SICAAS1034—SICAAS1039 2.99 0.85 9.41
2 qSPAD2 SICAAS2035—SICAAS2038 2.40 -0.86 9.77
5 qSPAD5.1 SICAAS5034—SICAAS5035 3.22 1.05 13.28
5 qSPAD5.2 SICAAS5035—SICAAS5036 2.94 0.84 8.27
8 qSPAD8.1 SICAAS8007—SICAAS8014 2.15 0.98 12.44
8 qSPAD8.2 SICAAS8014—SICAAS8019 2.41 1.02 12.64
正常氮+N 1 qSPAD1 SICAAS1034—SICAAS1039 3.57 1.11 13.47
9 qSPAD9.1 SICAAS9001—SICAAS9107 2.77 -0.73 5.67
9 qSPAD9.2 SICAAS9006—SICAAS9013 2.42 -0.76 5.40
低氮-N 1 qPNC1.1 SICAAS1060—SICAAS1057 2.87 0.12 8.77
1 qPNC1.2 SICAAS1057—SICAAS1052 2.51 0.10 6.78
2 qPNC2 SICAAS2046—SICAAS2016 2.90 0.09 6.04
3 qPNC3 SICAAS3043—SICAAS3048 2.40 0.99 6.82
5 qPNC5.1 SICAAS5083—SICAAS5034 4.44 0.17 16.92
5 qPNC5.2 SICAAS5034—SICAAS5035 5.03 0.18 20.80
6 qPNC6.1 SICAAS6019—SICAAS6005 2.50 -0.10 6.96
6 qPNC6.2 SICAAS6055—SICAAS6008 2.79 -0.12 9.06
正常氮+N 2 qPNC2 SICAAS2053—SICAAS2020 2.01 -0.16 8.84
8 qPNC8 SICAAS8014—SICAAS8019 2.82 0.18 9.62

Fig. 3

Chromosomal positions of QTLs for traits related to low nitrogen resistance Hollow symbols indicated that the N application was -N; Solid symbols indicated that the N application was +N"

Table 4

Annotation of candidate genes"

Candidate genes
KO annotation
GO annotation
Functional annotation
qMRL1.1 1 Seita.1G121100 K18482 GO:0004084 D-氨基酸转氨酶
D-amino-acid transaminase
qMRL3 3 Seita.3G051900 GO:0006808 氮利用调控蛋白P-Ⅱ
Nitrogen regulatory protein P-Ⅱ
qMRL5.1 5 Seita.5G068000 K14638 GO:0015333 蛋白NRT1/PTR6.1家族
Protein NRT1/PTR FAMILY 6.1
qMRL5.2 5 Seita.5G400900 K14209 GO:0003333 氨基酸透性酶第8亚家族
Amino acid permease 8
qSPAD1 1 Seita.1G121100 K18482 GO:0004084 D-氨基酸转氨酶
D-amino-acid transaminase
qSPAD5.1 5 Seita.5G400900 K14209 GO:0003333 氨基酸透性酶第8亚家族
Amino acid permease 8
qRDW3 3 Seita.3G051900 GO:0006808 氮利用调控蛋白P-Ⅱ
Nitrogen regulatory protein P-Ⅱ
qRDW6 6 Seita.6G078400 K19476 GO:0016021 赖氨酸组氨酸转运子1
Lysine histidine transporter 1
qRDW9 9 Seita.9G477200 K14638 GO:0022857 蛋白NRT1/PTR8.3家族
Protein NRT1/PTR FAMILY 8.3
qSDW3 3 Seita.3G051900 GO:0006808 氮利用调控蛋白P-Ⅱ
Nitrogen regulatory protein P-Ⅱ
qSDW5.1 5 Seita.5G068000 K14638 GO:0015333 蛋白NRT1/PTR6.1家族
Protein NRT1/PTR FAMILY 6.1
qSDW6.1 6 Seita.6G078400 K19476 GO:0016021 赖氨酸组氨酸转运子1
Lysine histidine transporter 1
qPDW3 3 Seita.3G051900 GO:0006808 氮利用调控蛋白P-Ⅱ
Nitrogen regulatory protein P-Ⅱ
qPNC3 3 Seita.3G051900 GO:0006808 氮利用调控蛋白P-Ⅱ
Nitrogen regulatory protein P-Ⅱ
qPNC5.1 5 Seita.5G068000 K14638 GO:0015333 蛋白NRT1/PTR6.1家族
Protein NRT1/PTR FAMILY 6.1
qPNC5.2 5 Seita.5G400900 K14209 GO:0003333 氨基酸透性酶第8亚家族
Amino acid permease 8
qPNC6.2 6 Seita.6G078400 K19476 GO:0016021 赖氨酸组氨酸转运子1
Lysine histidine transporter 1
qPH5.3 5 Seita.5G068000 K14638 GO:0015333 蛋白NRT1/PTR6.1家族
Protein NRT1/PTR FAMILY 6.1
qPH6 6 Seita.6G078400 K19476 GO:0016021 赖氨酸组氨酸转运子1
Lysine histidine transporter 1
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