黄瓜单性结实性状遗传与QTL定位

doi:10.3864/j.issn.0578-1752.2020.01.015

摘要/Abstract

摘要：

【目的】单性结实性是影响设施黄瓜产量和品质的重要性状。深入解析黄瓜单性结实性状遗传规律并对其进行QTL定位,有助于提高设施专用黄瓜品种育种效率。【方法】以强单性结实自交系‘6457’和弱单性结实自交系‘6426’构建的重组自交系F_2:8为材料,基于3年表型数据,采用黄瓜基因组测序SSR分子标记构建黄瓜遗传连锁图谱,结合QTL-Seq分析,对黄瓜单性结实性进行QTL定位。【结果】黄瓜单性结实性状符合数量遗传特征。利用SSR标记构建了1张包含11个连锁群的遗传图谱,覆盖基因组555.0 cM,平均图距为6.8 cM。2016—2018年春季在3号染色体上均检测到1个与黄瓜单性结实性相关的QTL位点,位于标记SSR19430和SSR15419之间（3.33—5.57 Mb）,遗传距离6.6 cM,贡献率分别为11%、12.5%和6.3%。进一步进行QTL-Seq分析,发现4个与黄瓜单性结实性相关的QTL,分别位于1号（4.38—11.00 Mb）、3号（2.24—10.66 Mb）、6号（15.67—17.93 Mb,26.33—27.49 Mb）染色体上。其中在3号染色体上检测到的QTL与Map QTL所得的QTL区间重叠。推测Csa3G047740、Csa3G073810、Csa3G043910和Csa6G362930为与黄瓜单性结实性状相关的候选基因。【结论】分别在1、3、6号染色体上检测到4个与黄瓜单性结实性相关的QTL位点,其中3号染色体上的QTL年度间稳定,贡献率较高。

关键词: 黄瓜, 单性结实, 遗传图谱, QTL定位

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 F_2:8 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

牛志红,宋晓飞,李晓丽,郭晓雨,何书强,贺栾劲芝,冯志红,孙成振,闫立英. 黄瓜单性结实性状遗传与QTL定位[J]. 中国农业科学, 2020, 53(1): 160-171.

ZhiHong NIU,XiaoFei SONG,XiaoLi LI,XiaoYu GUO,ShuQiang HE,LuanJingZhi HE,ZhiHong FENG,ChengZhen SUN,LiYing YAN. Inheritance and QTL Mapping for Parthenocarpy in Cucumber[J]. Scientia Agricultura Sinica, 2020, 53(1): 160-171.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2020.01.015

https://www.chinaagrisci.com/CN/Y2020/V53/I1/160

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表3

黄瓜单性结实性状相关候选基因和功能预测"

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

表3

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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 (%)	Q_phred值 Q20 (%)	Q_phred值 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

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