Scientia Agricultura Sinica ›› 2020, Vol. 53 ›› Issue (1): 160-171.doi: 10.3864/j.issn.0578-1752.2020.01.015

• SPECIAL FOCUS: MOLECULAR BIOLOGY OF CUCUMBER • Previous Articles     Next Articles

Inheritance and QTL Mapping for Parthenocarpy in Cucumber

ZhiHong NIU,XiaoFei SONG,XiaoLi LI,XiaoYu GUO,ShuQiang HE,LuanJingZhi HE,ZhiHong FENG,ChengZhen SUN(),LiYing YAN()   

  1. Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei
  • Received:2019-01-21 Accepted:2019-06-05 Online:2020-01-01 Published:2020-01-19
  • Contact: ChengZhen SUN,LiYing YAN E-mail:chengzhensun@126.com;yanliying2017@126.com

Abstract:

【Objective】 Parthenocarpy is an important trait affecting both yield and quality in the protected cucumber production. Genetic analysis of parthenocarpy and its QTL mapping are of great significance for improving breeding efficiency in cucumber.【Method】 Based on three-year phenotypic data, the genetic linkage map of cucumber was constructed by using SSR molecular markers obtained from cucumber genome sequencing, and the QTL-Seq analysis was used to map the parthenocarpy of cucumber, using recombinant inbred line F2:8 constructed from strong parthenocarpic inbred line ‘6457’ and weak parthenocarpic inbred line ‘6426’.【Result】 The inheritance of parthenocarpy in cucumber accorded with quantitative inheritance. A genetic map containing 11 linkage groups was constructed using SSR markers, covering 555.0 cM of the genome with an average distance of 6.8 cM. In the spring of 2016, 2017 and 2018, a single QTL locus related to parthenocarpy was commonly detected between SSR19430 and SSR15419 markers (3.33-5.57 Mb) on chromosome 3, and the genetic distance was 6.6 cM, with 11%, 12.5% and 6.3% contribution rate, respectively. By QTL-Seq analysis, four QTLs related to parthenocarpy were identified on chromosomes 1 (4.38-11.00 Mb), 3 (2.24-10.66 Mb) and 6 (15.67-17.93 Mb; 26.33-27.49 Mb), the QTL on chromosome 3 overlapped with that detected by Map QTL approach. Csa3G047740, Csa3G073810, Csa3G043910 and Csa6G362930 were proposed to be candidate genes associated with parthenocarpic trait in cucumber. 【Conclusion】Four QTLs were identified on chromosome 1, 3 and 6, including one QTL on chromosome 3 that was consistently detected over years with relatively high contribution. The results could facilitate marker-assisted selection and understanding the underlying mechanism of parthenocarpy in cucumber.

Key words: cucumber, parthenocarpy, genetic map, QTL mapping

Fig. 1

Distribution of average parthenogenetic fruit setting percentage per line in the spring of 2016, 2017 and 2018"

Fig. 2

SSR genetic linkage group and QTL mapping of parthenocarpy in the cucumber (‘6457’ב6426’)"

Fig. 3

QTL mapping on chromosome 3 of parthenocarpy in the cucumber (‘6457’ב6426’) on the spring of 2016 (A) , 2017 (B) and 2018 (C)"

Table 1

Quality control of re-sequencing data of QTL-Seq for parthenocarpy in the cucumber (‘6457’× ‘6426’)"

样品
Sample
原始数据
Raw base (bp)
有效数据
Clean base (bp)
有效率
Effective rate (%)
碱基错误率
Error rate (%)
Qphred
Q20 (%)
Qphred
Q30 (%)
GC含量
GC content (%)
P1 5376170100 5069987400 94.30 0.03 96.68 92.68 38.92
np 8447689500 7672464900 88.11 0.04 93.99 87.01 39.84
P2 4140457200 4004934600 96.73 0.03 96.88 93.12 39.20
par 6980472300 6819972600 97.70 0.03 95.03 89.38 38.80

Table 2

Sequencing depth and coverage analysis of QTL-Seq for parthenocarpy in the cucumber (‘6457’ב6426’)"

样品类型
Sample
Reads比对数
Mapped reads
Reads总数
Total reads
比对率
Mapping rate (%)
样品平均覆盖深度
Average depth (X)
1X数据覆盖比率
Coverage at least 1X (%)
4X数据覆盖比率
Coverage at least 4X (%)
P1 29754479 33799916 88.03 15.27 98.12 92.06
P2 23533219 26699564 88.14 12.40 97.21 86.53
par 39918316 45466484 87.80 20.24 98.65 95.70
np 44530059 51149766 87.06 21.61 98.70 95.57

Fig. 4

Distribution of SNP-index on chromosomes for parthenocarpy in cucumber (‘6457’× ‘6426’) A: The distribution of SNP-index on chromosomes parthenocarpy pools; B: The distribution of SNP-index on chromosomes in non-parthenocarpy pools; C: The distribution of Delta SNP-index on chromosomes, significant QTLs are marked with open boxes"

Fig. 5

Overlaping of Map QTL (red box) and QTL-Seq (blue box) on chromosome 3 for parthenocarpy in cucumber (‘6457’× ‘6426’)"

Table 3

Candidate genes prediction and function annotations for parthenocarpy in cucumber"

基因号
Gene ID
变异类型
Variant
位置
Position
参考基因组基因型/该位点其他基因型Ref/Alt 拟南芥库里功能注释
Functional annotation of Arabidopsis
Csa1G042220 Nonsynonymous 4159708 T/C 编码ASPG1,与抗旱相关Encodes ASPG1 (ASPARTIC PROTEASE IN GUARD CELL 1).
Functions in drought avoidance through abscisic acid (ABA) signalling in guard cells
Csa1G049980 Nonsynonymous 5680530 A/G 肽酶C78,泛素折叠修饰特异性肽酶1/2
Peptidase C78, ubiquitin fold modifier-specific peptidase 1/2
Csa6G367130 Nonsynonymous 16841983 C/G 靶圈套卷曲螺旋结构域蛋白 Target SNARE coiled-coil domain protein
Csa1G042830 Upstream 4532431 A/G 钙依赖性脂质结合(CALB结构域)家族蛋白
Calcium-dependent lipid-binding (CaLB domain) family protein
Csa1G045620 Upstream 5048161 T/C 编码钙依赖性蛋白激酶 Target SNARE coiled-coil domain protein
Csa1G045620 Upstream 5048182 T/C 编码钙依赖性蛋白激酶 Target SNARE coiled-coil domain protein
Csa1G045620 Upstream 5048193 G/A 编码钙依赖性蛋白激酶 Target SNARE coiled-coil domain protein
Csa1G045620 Upstream 5048246 G/A 编码钙依赖性蛋白激酶 Target SNARE coiled-coil domain protein
Csa3G002320 Upstream 239366 G/C RB1诱导的卷曲螺旋蛋白 RB1-inducible coiled-coil protein
Csa3G036410 Upstream 2537701 C/T 富含亮氨酸的重复蛋白激酶家族蛋白
Leucine-rich repeat protein kinase family protein
Csa3G043910 Upstream 3022472 A/G GRAS家族转录因子 GRAS family transcription factor
Csa3G043910 Upstream 3022485 T/A GRAS家族转录因子 GRAS family transcription factor
Csa3G045170 Upstream 3188752 T/C 跨膜蛋白 Transmembrane protein
Csa3G047740 Upstream 3294577 C/T 咖啡酸/5-羟阿魏酸O-甲基转移酶
A caffeic acid/5-hydroxyferulic acid O-methyltransferase
Csa3G047740 Upstream 3294578 G/A 咖啡酸/5-羟阿魏酸O-甲基转移酶
A caffeic acid/5-hydroxyferulic acid O-methyltransferase
Csa3G073810 Upstream 3855792 G/A 编码参与介导植物对发病机制的反应的蛋白质
Encodes a protein involved in mediating plant responses to pathogenesis
Csa3G144130 Upstream 9538626 G/A 编码与CBL相互作用蛋白激酶SNF1和SOS2具有相似性的丝氨酸/苏氨酸蛋白激酶
Encodes a serine/threonine protein kinase with similarities to CBL-interacting protein kinases, SNF1 and SOS2
Csa3G144130 Upstream 9538714 G/A 编码与CBL相互作用蛋白激酶SNF1和SOS2具有相似性的丝氨酸/苏氨酸蛋白激酶
Encodes a serine/threonine protein kinase with similarities to CBL-interacting protein kinases, SNF1 and SOS2
Csa6G324800,Csa6G324810 Upstream 15102611 C/G 编码与NAD相关的苹果酸脱氢酶活性的蛋白
Encodes a protein with NAD-dependent malate dehydrogenase activity, located in chloroplasts
Csa6G344310 Upstream 15681038 A/G 腺苷酸核苷酸水解酶类似结构域蛋白的激酶
Kinase with adenine nucleotide alpha hydrolases-like domain-containing protein
Csa6G344310 Upstream 15681043 T/C 腺苷酸核苷酸水解酶类似结构域蛋白的激酶
Kinase with adenine nucleotide alpha hydrolases-like domain-containing protein
Csa6G362930 Upstream 16350065 A/C 亚精胺合成酶 Encodes a spermine synthase
Csa6G375720 Upstream 16932936 T/C 抗病蛋白(CC-NBS-LRR类)家族
Disease resistance protein (CC-NBS-LRR class) family
Csa6G375720 Upstream 16932970 A/G 抗病蛋白(CC-NBS-LRR类)家族
Disease resistance protein (CC-NBS-LRR class) family
Csa6G396650 Upstream 17566966 C/T 编码一种调节细菌肽聚糖传感和对细菌感染免疫的赖氨酸基序蛋白
Encodes a lysin-motif protein mediating bacterial peptidoglycan sensing and immunity to bacterial infection
Csa6G513690 Upstream 26648579 A/C 编码参与苯丙氨酸生物合成的质体局部芳香族脱水酶
Encodes a plastid-localized arogenate dehydratase involved in phenylalanine biosynthesis
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