Quantitative Trait Locus Mapping and Analysis of Traits Related to Flower，Fruit，and Leaf in Loquat

doi:10.16420/j.issn.0513-353x.2023-0500

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (6): 1189-1200.doi: 10.16420/j.issn.0513-353x.2023-0500

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Quantitative Trait Locus Mapping and Analysis of Traits Related to Flower，Fruit，and Leaf in Loquat

ZHAO Chongbin¹, ZHANG Weiyin¹, LI Shuqing¹, GUO Yihan¹, XU Hongxia², CHEN Junwei²^,^**(), YANG Xianghui¹^,^**(), PENG Ze¹^,^**()

¹ College of Horticulture，South China Agricultural University，Key Laboratory of Biology and Genetic Improvement of Horticultural Crops（South China），Ministry of Agriculture and Rural Affairs，Guangzhou 510642，China
² Institute of Horticulture，Zhejiang Academy of Agricultural Sciences，Hangzhou 310021，China

Received:2023-09-11 Revised:2023-11-21 Online:2024-12-18 Published:2024-06-21
Contact: CHEN Junwei, YANG Xianghui, PENG Ze

Abstract

Abstract:

The study focused on an F₁ population of 130 individuals from the cross between‘Ninghaibai’×‘Oobusa’loquat cultivars. Based on a well-constructed high-density genetic map of loquat，QTL mapping was performed for 17 fruit-，leaf- and floral-related traits，and candidate genes were screened from the key QTL intervals. The results showed significant correlations exceeding the significance level among multiple traits. A total of 153 QTLs were identified for the 17 traits. Nine traits，including transverse diameter，flesh thickness，seed number，seed weight，fruit shape index，width of leaf blade，length of leaf blade，width of leaf blade，and shape of leaf base，had QTLs with phenotypic variance explained rates of above 25%. Notably，six QTL intervals on LG4（13.500-14.276 cM and 23.646-24.804 cM），LG8（0-8.851 cM），LG12（41.198-45.852 cM and 65.246-66.407 cM），and LG15（92.921-95.244 cM），were shared among six or more traits，with phenotypic variance explained rates above 35% for multiple traits. Furthermore，a total of 13 candidate genes related to plant growth and development，cell division，cell expansion，and plant hormone regulation were obtained from the overlapping intervals of LG12（41.198-45.852 cM）and LG15（92.921-95.244 cM）.

Key words: loquat, Eriobotrya japonica, fruit, leaf, flower, trait, QTL mapping, candidate gene

ZHAO Chongbin, ZHANG Weiyin, LI Shuqing, GUO Yihan, XU Hongxia, CHEN Junwei, YANG Xianghui, PENG Ze. Quantitative Trait Locus Mapping and Analysis of Traits Related to Flower，Fruit，and Leaf in Loquat[J]. Acta Horticulturae Sinica, 2024, 51(6): 1189-1200.

Figures/Tables 9

References 40

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叶面形态 Leaf blade	叶姿 Leaf attitude	花支轴紧密度 Density of secondary peduncles	叶形 Leaf shape	叶基形状 Shape of leaf base	赋值 Assignment
平展Flat	斜向上Upward	紧密Dense	披针形Lanceolate	渐狭形Narrowly cuneate	1
稍皱Rugulose	平伸Outward	中等Medium	椭圆形Elliptic	楔形Cuneate	2
皱Ruguse	斜向下Downward	疏散Sparse	倒卵形Obovoid	宽楔形Broadly cuneate	3

叶面形态 Leaf blade	叶姿 Leaf attitude	花支轴紧密度 Density of secondary peduncles	叶形 Leaf shape	叶基形状 Shape of leaf base	赋值 Assignment
平展Flat	斜向上Upward	紧密Dense	披针形Lanceolate	渐狭形Narrowly cuneate	1
稍皱Rugulose	平伸Outward	中等Medium	椭圆形Elliptic	楔形Cuneate	2
皱Ruguse	斜向下Downward	疏散Sparse	倒卵形Obovoid	宽楔形Broadly cuneate	3

性状 Trait	果纵径Longitudinal diameter （LD）	果横径Transverse diameter （TD）	果形指数Fruit shape index （FSI）	果肉厚 Flesh thickness （FT）	可溶性固形物Total soluble solids （TSS）	种子质量 Seed weight （SW）	种子数 Seed number （SN）	叶姿 Leaf attitude（LA）
LD	1
TD	0.735^**	1
FSI	0.248^**	-0.472^**	1
FT	0.766^**	0.822^**	-0.178^*	1
TSS	-0.440^**	-0.496^**	0.136	-0.493^**	1
SW	0.568^**	0.894^**	-0.532^**	0.517^**	-0.322^**	1
SN	0.016	0.440^**	-0.617^**	0.030	-0.114	0.647^**	1
LA	0.005	0.085	-0.110	0.122	-0.132	0.022	0.081	1
LS	-0.082	-0.093	0.022	-0.093	0.182^*	-0.089	-0.155	0.033
SLB	0.168	0.271^**	-0.160	0.231^*	-0.177^*	0.266^**	0.123	0.030
LBSUS	-0.197^*	-0.363^**	0.256^**	-0.191^*	0.197^*	-0.378^**	-0.163	-0.161
LLB	0.237^**	0.503^**	-0.414^**	0.234^**	-0.249^**	0.561^**	0.420^**	0.086
WLB	0.154	0.411^**	-0.397^**	0.185^*	-0.149	0.458^**	0.358^**	0.018
LP	0.357^**	0.493^**	-0.240^**	0.388^**	-0.263^**	0.469^**	0.189^*	0.034
LT	-0.034	0.030	-0.078	-0.014	0.083	0.069	0.118	0.022
DSP	0	0.102	-0.121	0.164	-0.064	0.065	0	-0.115
FCW	0.246^**	0.467^**	-0.330^**	0.377^**	-0.183^*	0.442^**	0.163	0.037
性状 Trait	叶形 Leaf shape （LS）	叶基形状Shape of leaf base（SLB）	叶面形态Leaf blade：Shape of upper side （LBSUS）	叶片长 Length of leaf blade（LLB）	叶片宽 Width of leaf blade（WLB）	叶柄长Length of petiole （LP）	叶片厚 Leaf thickness （LT）	花支轴紧密度Density of secondary peduncles（DSP）	花序宽Flower cluster width（FCW）
LS	1
SLB	-0.123	1
LBSUS	-0.059	-0.034	1
LLB	0.024	0.052	-0.480^**	1
WLB	0.269^**	-0.009	-0.355^**	0.866^**	1
LP	-0.054	0.03	-0.139	0.538^**	0.456^**	1
LT	-0.021	-0.057	-0.050	0.084	0.099	-0.091	1
DSP	0.002	0.042	0.063	0.117	0.131	0.226^*	0.008	1
FCW	0.057	0.146	-0.375^**	0.579^**	0.549^**	0.433^**	0.096	0.544^**	1

性状 Trait	果纵径Longitudinal diameter （LD）	果横径Transverse diameter （TD）	果形指数Fruit shape index （FSI）	果肉厚 Flesh thickness （FT）	可溶性固形物Total soluble solids （TSS）	种子质量 Seed weight （SW）	种子数 Seed number （SN）	叶姿 Leaf attitude（LA）
LD	1
TD	0.735^**	1
FSI	0.248^**	-0.472^**	1
FT	0.766^**	0.822^**	-0.178^*	1
TSS	-0.440^**	-0.496^**	0.136	-0.493^**	1
SW	0.568^**	0.894^**	-0.532^**	0.517^**	-0.322^**	1
SN	0.016	0.440^**	-0.617^**	0.030	-0.114	0.647^**	1
LA	0.005	0.085	-0.110	0.122	-0.132	0.022	0.081	1
LS	-0.082	-0.093	0.022	-0.093	0.182^*	-0.089	-0.155	0.033
SLB	0.168	0.271^**	-0.160	0.231^*	-0.177^*	0.266^**	0.123	0.030
LBSUS	-0.197^*	-0.363^**	0.256^**	-0.191^*	0.197^*	-0.378^**	-0.163	-0.161
LLB	0.237^**	0.503^**	-0.414^**	0.234^**	-0.249^**	0.561^**	0.420^**	0.086
WLB	0.154	0.411^**	-0.397^**	0.185^*	-0.149	0.458^**	0.358^**	0.018
LP	0.357^**	0.493^**	-0.240^**	0.388^**	-0.263^**	0.469^**	0.189^*	0.034
LT	-0.034	0.030	-0.078	-0.014	0.083	0.069	0.118	0.022
DSP	0	0.102	-0.121	0.164	-0.064	0.065	0	-0.115
FCW	0.246^**	0.467^**	-0.330^**	0.377^**	-0.183^*	0.442^**	0.163	0.037
性状 Trait	叶形 Leaf shape （LS）	叶基形状Shape of leaf base（SLB）	叶面形态Leaf blade：Shape of upper side （LBSUS）	叶片长 Length of leaf blade（LLB）	叶片宽 Width of leaf blade（WLB）	叶柄长Length of petiole （LP）	叶片厚 Leaf thickness （LT）	花支轴紧密度Density of secondary peduncles（DSP）	花序宽Flower cluster width（FCW）
LS	1
SLB	-0.123	1
LBSUS	-0.059	-0.034	1
LLB	0.024	0.052	-0.480^**	1
WLB	0.269^**	-0.009	-0.355^**	0.866^**	1
LP	-0.054	0.03	-0.139	0.538^**	0.456^**	1
LT	-0.021	-0.057	-0.050	0.084	0.099	-0.091	1
DSP	0.002	0.042	0.063	0.117	0.131	0.226^*	0.008	1
FCW	0.057	0.146	-0.375^**	0.579^**	0.549^**	0.433^**	0.096	0.544^**	1

性状 Trait	QTL数量 QTL number	涉及连锁群 Involved LG	贡献率/% Explain rate	LOD (0.995)
果横径Transverse diameter	26	LG3、LG4、LG8、LG10、LG12、LG14、LG15、LG16、LG17	19.4 ~ 56.9	6.1
果纵径Longitudinal diameter	8	LG8、LG12、LG15、	18.3 ~ 22.2	5.7
果肉厚Flesh thickness	15	LG4、LG8、LG12、LG14、LG15、LG17	18.0 ~ 28.1	5.6
可溶性固形物Total soluble solids	1	LG12	19.4 ~ 20.3	6.0
种子质量Seed weight	20	LG3、LG4、LG8、LG10、LG12、LG14、LG15、LG16、LG17	17.7 ~ 61.5	5.5
种子数Seed number	14	LG4、LG8、LG12、LG16	18.7 ~ 25.5	5.8
果形指数Fruit shape index	11	LG3、LG4、LG8、LG12、LG14、LG15、LG16	18.1 ~ 35.8	5.6
花序支轴紧密度 Density of secondary peduncles	2	LG6、LG14	9.1 ~ 9.8	2.5
花序宽Flower cluster width	7	LG4、LG8、LG12、LG15	19.6 ~ 25.5	5.8
叶姿Leaf attitude	2	LG10、LG12	10.6 ~ 12.2	3.0
叶面形态 Leaf blade：Shape of upper side	1	LG12	22.9 ~ 23.9	6.4
叶形Leaf shape	2	LG4	10.0 ~ 11.9	3.0
叶片厚Leaf thickness	1	LG1	20.0	5.6
叶片长Length of leaf blade	9	LG3、LG4、LG8、LG12、LG15	19.9 ~ 37.5	5.9
叶柄长Length of petiole	2	LG12、LG16	19.7 ~ 22.2	5.8
叶基形状Shape of leaf base	24	LG3、LG4、LG8、LG10、LG12、LG15、LG16	19.2 ~ 41.7	5.7
叶片宽Width of leaf blade	8	LG8、LG12、LG15	21.2 ~ 30.7	6.3

Quantitative Trait Locus Mapping and Analysis of Traits Related to Flower，Fruit，and Leaf in Loquat

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连锁群 LG	重合区间/cM Overlapping intervals	标记数量 Marker number	性状 Trait	对应的QTL Corresponding QTL
4	13.500 ~ 14.276	2	花序宽、果形指数、叶片长、叶基形状、种子质量、果横径 Flower cluster width，fruit shape index，length of leaf blade，shape of leaf base，seed weight，transverse diameter	FCW.4.1、FSI.4.3、LLB.4.1、SLB.4.1、SW.4.1、TD.4.3
	23.646 ~ 24.804	5	果形指数、果肉厚、叶片长、叶基形状、种子质量、果横径 Fruit shape index，flesh thickness，length of leaf blade，shape of leaf base，seed weight，transverse diameter	FSI.4.3、FT.4.1、LLB.4.1、SLB.4.1、SW.4.1、TD.4.3
8	0 ~ 8.851	5	果形指数、果肉厚、果纵径、叶片长、叶基形状、种子质量、果横径 Fruit shape index，flesh thickness，longitudinal diameter，length of leaf blade，shape of leaf base，seed weight，transverse diameter	FSI.8.1、FT.8.1、LD.8.1、LLB.8.1、SLB.8.1、SW.8.1、TD.8.1
12	41.198 ~ 45.852	13	花序宽、果形指数、果肉厚、叶片长、叶柄长、叶基形状、种子数、种子质量、果横径、叶片宽 Flower cluster width，fruit shape index，flesh thickness，length of leaf blade，length of petiole，shape of leaf base，seed number，seed weight，transverse diameter，width of leaf blade	FCW.12.1、FSI.12.2、FT.12.3、LLB.12.1、LP.12.1、SLB.12.1、SN.12.1、SW.12.1、TD.12.1、WLB.12.1
	65.246 ~ 66.407	7	果形指数、果肉厚、叶片长、叶基形状、种子数、种子质量、果横径、叶片宽 Fruit shape index，flesh thickness，length of leaf blade，shape of leaf base，seed number，seed weight，transverse diameter，width of leaf blade	FSI.12.2、FT.12.3、LLB.12.1、SLB.12.1、SN.12.1、SW.12.1、TD.12.1、WLB.12.3
15	92.921 ~ 95.244	15	花序宽、果形指数、果肉厚、叶片长、叶基形状、种子质量、果横径、叶片宽 Flower cluster width，fruit shape index，flesh thickness，length of leaf blade，shape of leaf base，seed weight，transverse diameter，width of leaf blade	FCW15.2、FSI15.1、FT.15.1、LLB15.1、SLB.15.6、SW.15.2、TD.15.2、WLB15.2

性状 Trait	LG4： 13.500 ~ 14.276 cM	LG4： 23.646 ~ 24.804 cM	LG8： 0 ~ 8.851 cM	LG12： 41.198 ~ 45.852 cM	LG12： 65.246 ~ 66.407 cM	LG15： 92.921 ~ 95.244 cM
叶基形状 Shape of leaf base	26.1 ~ 27.4	22.3 ~ 23.3	38.7 ~ 41.7	35.9 ~ 37.1	27.7 ~ 28.8	31.5 ~ 34.2
种子质量 Seed weight	30.4 ~ 31.4	37.6 ~ 39.9	54.7 ~ 56.0	58.0 ~ 58.8	42.8 ~ 45.3	45.4 ~ 47.0
果横径 Transverse diameter	24.4 ~ 25.9	35.9 ~ 38.1	50.7 ~ 51.7	54.4 ~ 55.7	42.5 ~ 46.6	45.7 ~ 46.1
叶片长Length of leaf blade	20.2 ~ 21.6	23.1 ~ 25.2	27.5 ~ 30.2	36.0 ~ 37.5	29.4 ~ 31.0	29.1 ~ 30.2
果形指数Fruit shape index	18.5 ~ 20.5	23.9 ~ 24.7	22.4 ~ 24.4	30.2 ~ 30.7	25.1 ~ 30.3	24.3 ~ 25.0
果肉厚 Flesh thickness		19.6 ~ 19.4	24.4 ~ 24.9	26.0 ~ 27.3	20.7 ~ 23.4	23.9 ~ 26.2
叶片宽Width of leaf blade				27.5 ~ 28.7	23.5 ~ 24.7	22.6 ~ 23.1
花序宽Flower cluster width	19.9 ~ 22.0			22.2 ~ 23.9		20.3 ~ 21.5
种子数 Seed number				21.5 ~ 22.3	21.6 ~ 24.5
叶柄长Length of petiole				19.7 ~ 22.2
果纵径 Longitudinal diameter			19.2 ~ 19.4

连锁群 LG	重合区间/cM Overlapping intervalsl	基因数 Gene number	注释Annotation					总计Total
连锁群 LG	重合区间/cM Overlapping intervalsl	基因数 Gene number	COG	GO	KEGG	Swiss-Prot	Nr	总计Total
4	13.500 ~ 14.276	0	0	0	0	0	0	0
	23.646 ~ 24.804	0	0	0	0	0	0	0
8	0 ~ 8.851	0	0	0	0	0	0	0
12	41.198 ~ 45.852	163	56	72	53	103	157	157
	65.246 ~ 66.407	27	9	13	8	15	27	27
15	92.921 ~ 95.244	24	3	5	7	12	24	24

QTL簇 QTL clusters	区间/cM Interval	QTL	候选基因ID Candidate gene ID	功能注释 Function annotation
12	41.198 ~ 45.852	SW.12.1 SLB.12.1 TD.12.1 FT.12.3 LLB.12.1 FSI.12.2 WLB.12.1 FCW.12.1 SN.12.1 LP.12.1	EVM0026248.1	含螺旋结构域蛋白SCD2 Coiled-coil domain-containing protein SCD2
			EVM0016634.2	CRC结构域蛋白TSO1 CRC domain-containing protein TSO1
			EVM0021421.1	F-box蛋白At1g55000 F-box protein At1g55000
			EVM0021006.1	FRIGIDA-like蛋白1 FRIGIDA-like protein 1
			EVM0036521.1	FRIGIDA-like蛋白3 FRIGIDA-like protein 3
			EVM0002631.1	赤霉素受体GID1C Gibberellin receptor GID1C
			EVM0014419.1	谷胱甘肽合成酶，叶绿体（前体） Glutathione synthetase，chloroplastic（precursor）
			EVM0007148.1	富甘氨酸RNA结合蛋白RZ1A Glycine-rich RNA-binding protein RZ1A
			EVM0008020.1	GTP结合蛋白At3g49725，叶绿体（前体） GTP-binding protein At3g49725，chloroplastic（precursor）
			EVM0003720.1	AUXIN RESPONSE 4蛋白 Protein AUXIN RESPONSE 4
15	92.921 ~ 95.244	SW.15.2 TD.15.2 SLB.15.6 LLB.15.1	EVM0039475.1	含硫氧还蛋白TTL1的TPR重复序列 TPR repeat-containing thioredoxin TTL1
			EVM0017898.1	含有甲基CpG结合结构域蛋白9
				Methyl-CpG-binding domain-containing protein 9
		FT.15.1 FSI.15.1 WLB.15.2 FCW.15.2	EVM0022488.1	Knotted-1-like 同源盒蛋白3 Homeobox protein knotted-1-like 3

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