藜麦基因组学与重要农艺性状位点研究进展

doi:10.16288/j.yczz.22-289

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Hereditas(Beijing) ›› 2022, Vol. 44 ›› Issue (11): 1009-1027.doi: 10.16288/j.yczz.22-289

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Progress on genomics and locus of important agronomic traits in Chenopodium quinoa

Linghong Li¹(), Tong Gou¹, Aixia Ren¹, Pengcheng Ding¹, Wen Lin¹, Xiangyun Wu², Min Sun¹(), Zhiqiang Gao¹

1. College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi
2. Shanxi Jiaqi Agri-Tech Co., Ltd., Taiyuan 030006, Shanxi

Received:2022-09-02 Revised:2022-10-10 Online:2022-11-20 Published:2022-10-27
Contact: Sun Min E-mail:lilinghong00en@163.com;sm_sunmin@126.com
Supported by:
the Fundamental Research Program of Shanxi Province(202103021223158);the Scientific Research Project of Shanxi Province Outstanding Doctoral Work Award Fund(SXBYKY2022022);the Doctoral research Project of Shanxi Agricultural University(2021BQ82)

Abstract

Abstract:

Quinoa (Chenopodium quinoa, Willd.) as a new health food in the 20th century, its comprehensive nutritional composition, stress resistance and other characteristics have been paid much of attention, and enjoys the reputation of “nutritional gold”, “vegetarian king” and “food in the future” in the world. In recent years, with the rapid development of genomics and high-throughput sequencing technology, the high-quality whole genome sequence of quinoa has been completed, and the omics analysis and functional research of a series of key genes have been gradually carried out. In this review, we summarize the research progress in quinoa genomics, gene family analysis of important transcription factors, genetic map construction, QTL mapping of important traits, and genes for important agronomic and yield traits. Moreover, according to the current status of quinoa breeding, this paper also put forward five key problems in quinoa breeding, and pointed out four important directions of genetic improvement and breeding of quinoa in the future, so as to provide reference for the realization of directional genetic improvement of quinoa in the future.

Key words: quinoa, genomics, genetic breeding, traits, genes

Linghong Li, Tong Gou, Aixia Ren, Pengcheng Ding, Wen Lin, Xiangyun Wu, Min Sun, Zhiqiang Gao. Progress on genomics and locus of important agronomic traits in Chenopodium quinoa[J]. Hereditas(Beijing), 2022, 44(11): 1009-1027.

Figures/Tables 5

Table 1

Identification and expression analysis of transcription factor gene family in quinoa"

名称	主要功能	成员数量(个)	组织表达特异性	基因功能预测
NAC	参与调节植物生长发育、次生代谢及胁迫反应	107	嫩芽、根中特异表达	AUR62036626、AUR620415254和AUR62043497可能参与藜麦对盐胁迫的响应与适应；AUR62029344可能参与盐胁迫抗性
MADS-box	参与调控植物花器官发育和开花过程的功能特性	103	花序、花	CqMADS33可能具有调控植物开花
WRKY	参与调控植物应对冻害、干旱、盐害等非生物胁迫与病原菌、虫害等生物胁迫反应	92	幼苗、茎、叶	CqWRKY18B-1、CqWRKY21A-1、CqWRKY51A-1和CqWRKY56A-2可能是重要的胁迫调节因子
TH	参与植物的生长发育和非生物胁迫响应	47	瘦果、花、叶片中高表达，根茎中低表达	CqTH36可能参与藜麦的抗逆；CqTH27和CqTH42可能也参与了藜麦花发育的调控
NHX	参与植物响应盐胁迫的过程	46	NA	推测35个NHXs基因，参与调控藜麦盐胁迫条件下的离子稳态和盐分分配
TCP	参与种子萌发、分枝发育、花叶发育、昼夜规律、激素反应及防御反应等过程的调控	31	叶、花蕾>茎、叶>根、花序、发育中的种子	TCP11基因在调控叶片发育及开花时间中发挥重要功能；CqTCP18.1基因参与调控分枝发育；CqTCP14在调控叶片发育及干旱胁迫中发挥一定作用；CqTCP15可能在种子萌发过程中发挥一定作用；CqTCP2.1基因可能调控叶片发育
SPL	参与植物由营养期向花期的过渡、花药发育、芽成熟、开花时期光信号的整合以及维持植物铜稳态等	23	花序>种子、叶片>茎>幼苗>根	AUR62011728和AUR62042534可能在干旱胁迫中发挥重要功能
Hsf	参与植物生长发育，能够响应多种不良逆境	23	幼苗、茎、叶、花序、干种子	CqHsf19在干种子中特异表达，可能在种子的发育和成熟过程中起特异的作用
GRF	参与植物生长、发育、代谢、繁殖、分化等多种生物学过程	18	种子>花序>根>幼苗>茎>叶片	AUR62013612和AUR62004236可能参与了藜麦花序的发育过程；AUR62002094和AUR62028212可能与藜麦产量性状有关
WOX	植物干细胞稳态维持、胚胎发生与胚胎后发育、激素信号转导、初生和次生物质代谢及抗逆响应	13	茎>种子和叶>幼苗	AUR62031363、AUR62003747和AUR62035466对氮胁迫有显著响应，可作为氮胁迫响应的候选基因
KEA	参与植物细胞钾离子的积累和平衡过程	10	几乎在所有组织中均有表达	AUR62027069和AUR62030910主要在地上部分发挥功能，可能参与维持植株正常生命活动中的离子稳态和K⁺利用；AUR62027477、AUR62033999、AUR62023671、AUR62021295、AUR62016085主要在地下部分发挥功能
FAX	参与质体中脂肪酸向外运输过程	10	在藜麦不同组织中均存在表达	AUR62006421、AUR62017596、AUR62026084和AUR62029770在种子中表达水平较高，可能在种子脂肪酸形成和积累中发挥着重要作用
NLP	参与植物氮素吸收、转运和同化过程	9	NA	AUR62007015、AUR62007012和AUR62019876可能在藜麦氮代谢途径中起重要调控作用

Table 1

Table 2

Table 3

Summary statistics of quantitative trait loci (QTL) in quinoa"

定位群体		性状	QTL名称	置信区间/遗传位置(cM)	R²(%)-性状	置信区间内基因数量
PI614889和CHEN-109 组建的F₂和F₃		DTF、PH、TKW	pleio4.1	69.10-64.44	22.01	104
PI614889和CHEN-109 组建的F₂和F₃		DTF、PH、TKW	pleio14.1	8.95-16.00	-	178
F₃		PH、PL、PD	pleio20.1	10.39-22.00	10.86	660
		DTF、PH、PD、TKW	pleio4.2	69.00-64.59	12.44	110
		DTM	dtm3.1	35.64-43.00	8.73	470
		MS	ms4.1	1.68-7.00	0.43	410
		MS	ms5.1	70.00-76.69	-	407
		PD	pd16.1	42.32-44.72	20.44	47
F₂		DTF、DTM、PH, PL、SW、SN、TKW	pleio4.3	59.62-62.00	16.21	88
		DTF、PH、PD、SW	pleio7.1	5.32-20.00	10.97	56
		SN	sn6.1	35.89-37.54	5.46	313
		TKW	tkw17.1	18.98-23.78	8.14	156
		皂苷	sap10.1	0.00-2.63	21.98	80
			sap13.1	14.61-20.93	-	262
			sap17.1	2.25-10.21	-	365
Atlas和Red Carina 组建的F₃群体		籽粒面积	AR-1	23.451	11.3	-
			AR-2	0	9.9	-
			AR-3	4.139	9.8	-
			AR-4	81.13	8.1	-
			AR-5	27.424	7.4	-
		花芽出现的时间	B-1	50.867	14.7	-
			B-2	0	14.4	-
			B-3	48.923	11.1	-
			B-4	85.2	9.4	-
			B-5	11.475	8.3	-
			B-6	80.933	7.5	-
		色相带1	C1-1	107.778	21.6	-
			C1-2	99.488	16.2	-
			C1-3	23.425	12.3	-
			C1-4	76.2	7.9	-
			C1-5	42.401	6.6	-
			C1-6	5.491	6.5	-
			C1-7	4.048	5.4	-
		色相带2 蓝光405~470 nm	C2-1	105.893	18.8	-
			C2-10	36.645	4.2	-
			C2-11	2	3.5	-
			C2-2	23.425	13.9	-
			C2-3	5.491	9.9	-
			C2-4	76.2	5.9	-
Atlas和Red Carina 组建的F₃群体		色相带2 蓝光405~470 nm	C2-5	99.488	5.1	-
			C2-6	42.401	5	-
			C2-7	28.244	4.7	-
			C2-8	4.27	4.4	-
			C2-9	38.069	4.3	-
		色相带3 绿光505~590 nm	C3-1	105.893	19.4	-
			C3-2	110.058	7.7	-
			C3-3	71.7	7.5	-
			C3-4	99.488	6.4	-
			C3-5	42.401	6	-
			C3-6	6.643	5.5	-
			C3-7	28.884	4.8	-
		色相带4 红光630~700 nm	C4-1	102.512	19.5	-
			C4-2	67.9	9.3	-
			C4-3	110.058	6.8	-
			C4-4	99.488	6.2	-
			C4-5	12.732	6	-
			C4-6	42.401	5.4	-
			C4-7	13.915	4.6	-
			C4-8	4.27	4.6	-
		色相带5 近红外光780 nm	C5-1	102.512	20.2	-
			C5-2	67.9	11.7	-
			C5-3	12.732	8.1	-
			C5-4	110.058	6	-
			C5-5	52.437	5.2	-
		色相带6 近红外光 850~890 nm	C6-1	102.512	11.9	-
			C6-2	52.437	11.1	-
			C6-3	12.732	9.5	-
			C6-4	116.223	8.5	-
			C6-5	67.9	7.9	-
			C6-6	11.828	7.6	-
			C6-7	110.058	7.1	-
			C6-8	91.849	5.8	-
		色相带7 近红外光 940~970 nm	C7-1	11.828	14.9	-
			C7-2	51.831	12	-
			C7-3	116.223	11.4	-
			C7-4	12.732	10.6	-
			C7-5	66.9	7.4	-
			C7-6	110.058	7.3	-
			C7-7	102.512	6.4	-
			C7-8	81.526	6.3	-
Atlas和Red Carina 组建的F₃群体	混合光系统A	CA-1	2.64	16.3	-
		CA-2	60.805	11.2	-
		CA-3	0	11.2	-
		CA-4	52.677	10.4	-
		CA-5	99.488	10.3	-
	混合光系统B	CB-1	9.892	12.5	-
		CB-2	107.778	11.5	-
		CB-3	9.784	11.1	-
		CB-4	0	11	-
		CB-5	6.643	9.1	-
		CB-6	29.702	8.2	-
		CB-7	3.01	7.9	-
		CB-8	7.649	7.8	-
	混合光系统L	CL-1	105.893	16.2	-
		CL-2	99.488	14.6	-
		CL-3	4.27	5.5	-
	开花时间	F9-1	19.698	14.4	-
		F9-2	110.2	13.9	-
		F9-3	3.484	11.5	-
		F9-4	16.18	9.1	-
	产量	G-1	65.4	15.5	-
		G-2	25.9	13.3	-
		G-3	40.797	12.9	-
		G-4	102.57	10.8	-
		G-5	7.102	10.2	-
		G-6	121.358	9.6	-
		G-7	32.724	9.2	-
		G-8	56.111	6.1	-
	种子颜色的色调	H-1	6.643	12.3	-
		H-2	107.778	9.8	-
		H-3	0	8.8	-
		H-4	81.539	7.7	-
		H-5	0	7.3	-
	种子颜色的性状强度	I-1	102.512	21.3	-
		I-10	4.27	4.4	-
		I-2	23.425	15.6	-
		I-3	30.776	8.1	-
		I-4	2	6.7	-
		I-5	99.488	6.3	-
		I-6	50.329	5.7	-
Atlas和Red Carina 组建的F₃群体	种子颜色的性状强度	I-7	40.374	5.6	-
		I-8	8.909	5.5	-
		I-9	67.9	5.2	-
	叶片颜色	LC-1	99.488	22.1	-
	叶片颜色	LC-2	110.058	10.6	-
	籽粒长度	LN-1	23.451	17.3	-
		LN-2	21.152	16.5	-
		LN-3	9.306	10.7	-
		LN-4	98.222	9.3	-
		LN-5	27.939	8.9	-
		LN-6	0	8	-
	残留菌体	RB-1	105.565	15.1	-
		RB-2	32.724	15.1	-
		RB-3	40.797	11.9	-
		RB-4	34.4	10.5	-
		RB-5	60.918	9.8	-
		RB-6	29.425	9.7	-
		RB-7	24.954	8.1	-
		RB-8	102.57	7.7	-
	性状饱和	S-1	110.006	19.4	-
	性状饱和	S-2	99.488	7.4	-
	千粒重	T-1	3.936	19.2	-
		T-2	41.433	18.9	-
		T-3	116.108	18.6	-
		T-4	27.125	13	-
		T-5	44.488	10.7	-
	籽粒宽度	W-1	81.13	13.4	-
		W-2	0	11.7	-
		W-3	23.451	11.2	-
		W-4	98.222	9.8	-

Table 3

Fig. 1

Table 4

Prediction of genes related to important traits in quinoa"

类别	性状	其他作物中已定位基因	藜麦中同源基因	所在染色体及物理位置 (Phytozome v1.0)	序列相似性(%)	表达部位
生长发育	早花	FT1(Beta vulgaris)	AUR62010060 (CqFT1A)	Chr.15:4930835-4933952	81.71	花
		FT1(Beta vulgaris)	AUR62013052 (CqFT1B)	Chr.17:79266951-79277600	92	花
		FT2 (Beta vulgaris)	AUR62000271 (CqFT2A)	Chr.12:3192361-3196369	82.12	叶片
			AUR62006619 (CqFT2B)	Chr.05:77596526-77601590	81.56	叶片
			AUR62033889	Chr.15:31458414-31465667	63.79	NA
农艺性状	株高	Rht-B1(Triticum aestivum)/ RGA1 (Arabidopsis	AUR62039523	Chr.06:26006908-26013645	59.3	NA
	株高	Rht-D1(Triticum aestivum)	AUR62014191	Chr.14:14625033-14626940	59.65	NA
	种子大小和数量	GIF1 (Oryza)	AUR62006205	Chr.15:3135695-3137782	60.21	NA
		DA2(Arabidopsis)/ GW2(Oryza)	AUR62041781	Chr.17:39742130-39752168	56.69/45.16	NA
		DA2(Arabidopsis)/ GW2(Oryza)	AUR62037970	Chr.05:34646253-34655250	56.66/45.57	NA
		AtCKX5(Arabidopsis)/ Gn1a (Oryza)	AUR62034531	Chr.10:7564646-7565207	68.67/43.49	NA
		AtCKX5(Arabidopsis)/ Gn1a (Oryza)	AUR62014467	Chr.03:4311653-74312220	68.67/44.01	NA
		AtCKX3 (Arabidopsis)/ Gn1a (Oryza)	AUR62029062	Chr.02:37236856-37237243	38.09/43.30	NA
		AtCKX3 (Arabidopsis)/ Gn1a (Oryza)	AUR62033955	Chr.00:184848685-184848904	35.82/41.65	NA
	落粒性	SHP1/SHP2 (Arabidopsis)	AUR62035850	Chr.02:11045541-11052900	68.64/67.93	NA
	落粒性	SHP1/SHP2 (Arabidopsis)	AUR62027653	Chr.01:128347481-128357581	65.68/64.98	NA
品质	皂苷合成	TSARL1 (Medicago truncatula)	AUR62017204	Chr.16:68549573-68551812	32	籽粒
	皂苷合成	TSARL2 (Medicago truncatula)	AUR62017206	Chr.16:68524854-68527010	30.86	根
	种子贮藏蛋白	11S (A.hypochondriacus)	11SA	NA	74	籽粒
	种子贮藏蛋白	11S (A.hypochondriacus)	11SB	NA	74	籽粒
非生物抗性	耐盐	SOS1	cqSOS1A	NA	NA	根
	耐盐	SOS1	cqSOS1B	NA	NA	根
	耐旱	NA	NA	NA	NA	NA
	耐热	HSFA1(Arabidopsis)	AUR62018674	Chr.16:76341712-76354887	52.89	NA
	耐热	HSFA1(Arabidopsis)	AUR62007327	Chr.13:2302837-2307436	50.87	NA
	耐冷	NA	NA	NA	NA	NA
	抗除草剂	AHAS	CqAHAS1-CqAHAS6	NA	NA	NA
	抗穗发芽	MFT(Arabidopsis)	AUR62029959	Chr.08:39671124-39679767	73.41	NA
			AUR62014698	Chr.01:29266367-29267601	49.13	NA
			AUR62012495	Chr.02:4594321-4597301	61.21	NA
			AUR62014699	Chr.01:29210009-29211182	60.47	NA
		MKK3 (Hordeumvulgare)	AUR62015864	Chr.05:956636-956737	62.03	NA
			AUR62026127	Chr.07:82092195-82092329	59.96	NA
			AUR62020359	Chr.12:56190719-56190853	62.55	NA
生物抗性	抗病	NA	NA	NA	NA	NA
生物抗性	抗虫	NA	NA	NA	NA	NA

Table 4

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定位群体	性状	物理区间(Mb)	染色体位置	候选基因
310份材料的全基因组测序	茎秆颜色	69.72-69.76	Cq1B	CqCYP76AD1/CqDODA1
	皂苷含量(mg/g)	8.85-9.20	Cq5B	AUR62017204/AUR62017206
	开花日数(天)	80.50-81.50	Cq2A	-
	成熟日数(天)	80.50-81.50	Cq2A	CqGLX2-2
	株高(cm)	80.50-81.50	Cq2A	-
	穗长(cm)	80.50-81.50	Cq2A	-
	千粒重(g)	63.20-64.87	Cq8B	CqPP2C/CqRING
	霉变敏感性	38.99-39.03	Cq2A	CqMTA/CqRGA2

Progress on genomics and locus of important agronomic traits in Chenopodium quinoa

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