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Molecular Breeding

, 39:18 | Cite as

QTL mapping for 11 agronomic traits based on a genome-wide Bin-map in a large F2 population of foxtail millet (Setaria italica (L.) P. Beauv)

  • Zhilan Wang
  • Jun WangEmail author
  • Jianxiang Peng
  • Xiaofen Du
  • Maoshuang Jiang
  • Yunfei Li
  • Fang Han
  • Guohua Du
  • Huiqing Yang
  • Shichao Lian
  • Jianpeng Yong
  • Wei Cai
  • Juduo Cui
  • Kangni Han
  • Feng Yuan
  • Feng Chang
  • Guobao Yuan
  • Wenna Zhang
  • Linyi Zhang
  • Shuzhong Peng
  • Hongfeng ZouEmail author
  • Erhu GuoEmail author
Article

Abstract

To identify quantitative trait loci (QTLs), a large F2 population in foxtail millet including 543 plants from a cross between Aininghuang and Jingu 21 was used to construct a high-density linkage map based on restriction site-associated DNA sequencing (RAD-seq). Based on the map, QTLs for 11 various agronomic traits, consisting of PH, PL, PD, PNL, FID, SID, PW, GW, TGW, PT and PC, were mapped. The map contained 3129 Bin markers from 48,790 single nucleotide polymorphisms (SNPs) spanning 1460.996 cM. Fifty-seven QTLs related to these 11 agronomic traits were detected using composite interval mapping (CIM), which explained 0.38–30.52% of total phenotypic variation explained (PVE). Among those, five major QTLs with a large PVE of more than 10%, including qPH5-2 for PH, qPD5-2 for PD, qPW5-1 for PW and qPC7-1 and qPC7-2 for PC, were detected. Notably, an extremely large effect QTL with a PVE of 30.52%, the qPH5-2 for PH, was observed. Furthermore, we newly developed five markers, which could be used for marker-assisted selection. Then, we verified these QTLs including qPC7-2 for PC, qPW5-1 for PW and qPH5-2 for PH were positive via correlation analysis of markers to traits in the natural population and the advanced generation population (AJF5) derived from the mapping population by single seed descent. Additionally, we found two multi-effect Mqtls, Mqtl5-2 and Mqtl2-5, underlying panicle development and yield, and one Mqtl, Mqtl1-2, probably related to plant growth and development by QTL prioritisation via Meta-QTL analysis. Moreover, we discussed candidate genes for the five major QTLs. Thus, mapping QTLs by RAD-seq using a large F2 population is efficient, and the present study offers valuable insights into the genetic basis of quantitative traits and marker-assisted selection in foxtail millet.

Keywords

Agronomic traits RAD-seq Bin-map QTL mapping Foxtail millet 

Abbreviations

CIM

Composite interval mapping

FID

First internode diameter

GW

Grain weight

PC

Pericarp colour

PD

Panicle diameter

PH

Plant height

PL

Panicle length

PNL

Panicle neck length

PT

Panicle type

PVE

Phenotypic variation explained

PW

Panicle weight

QTLs

Quantitative trait loci

RAD-seq

Restriction site-associated DNA sequencing

RFLP

Restriction fragment length polymorphism

SID

Second internode diameter

SNPs

Single nucleotide polymorphisms

SSR

Simple sequence repeat

SVs

Structure variants

TGW

Thousand grain weight

Notes

Acknowledgments

We thank René Boesten, from Wageningen University & Research, the Netherlands, for editing this manuscript.

Funding information

This research was supported by the Special Nonggu Research Project of Shanxi Academy of Agricultural Sciences (YCX2017D2201), the Shanxi Key Innovative Platform for germplasm enhancement and molecular breeding in major crops (201605D151002), the Shanxi Province Youth Fund (201701D221199), the Shanxi Key project of Key Research and Development Program (201703D211008), the Strategic Emerging Industries Program Support by the Shenzhen Municipal Government, the Basic Research Program Support by the Shenzhen Municipal Government (NO.JCY20150831201123287) and the China Agriculture Research System (CARS-06-13.5-A21).

Supplementary material

11032_2019_930_Fig4_ESM.png (759 kb)
Supplemental Figure S1

Distribution of agronomic traits of the F2 population (PNG 758 kb)

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High resolution image (TIF 1288 kb)
11032_2019_930_Fig5_ESM.png (5.8 mb)
Supplemental Figure S2

The panicle types in the F2 population (PNG 5985 kb)

11032_2019_930_MOESM2_ESM.tif (7.2 mb)
High resolution image (TIF 7354 kb)
11032_2019_930_Fig6_ESM.png (825 kb)
Supplemental Figure S3

The Bin genetic linkage map based on RAD-seq in foxtail millet (PNG 825 kb)

11032_2019_930_MOESM3_ESM.tif (976 kb)
High resolution image (TIF 975 kb)
11032_2019_930_Fig7_ESM.png (524 kb)
Supplemental Figure S4

Genetic distance versus physical distance for 48,790 single (PNG 523 kb) nucleotide polymorphisms (SNPs) in foxtail millet. The X-axis indicates the physical position of each SNP marker (in Mb); the Y-axis indicates the genetic position of each SNP marker (in cM). Red dots indicate the genetic position against the reference physical position (TIF 1141 kb)

11032_2019_930_MOESM4_ESM.tif (1.1 mb)
High resolution image (PNG 23958 kb) (TIF 1141 kb)
11032_2019_930_Fig8_ESM.png (23.4 mb)
Supplementary Figure S5

Meta-QTLs for multiple traits in foxtail millet (PNG 23958 kb)

11032_2019_930_MOESM5_ESM.tif (12.1 mb)
High resolution image (TIF 12367 kb)
11032_2019_930_MOESM6_ESM.xls (62 kb)
Supplementary Table 1 (XLS 61 kb)
11032_2019_930_MOESM7_ESM.xls (22 kb)
Supplementary Table 2 (XLS 21 kb)
11032_2019_930_MOESM8_ESM.partial (302 kb)
Supplementary Table 3 (PARTIAL 302 kb)
11032_2019_930_MOESM9_ESM.xls (26 kb)
Supplementary Table 4 (XLS 25 kb)
11032_2019_930_MOESM10_ESM.xls (162 kb)
Supplementary Table 5 (XLS 162 kb)
11032_2019_930_MOESM11_ESM.xlsx (12 kb)
Supplementary Table 6 (XLSX 11 kb)
11032_2019_930_MOESM12_ESM.xls (24 kb)
Supplementary Table 7 (XLS 24 kb)
11032_2019_930_MOESM13_ESM.xlsx (12 kb)
Supplementary Table 8 (XLSX 12 kb)
11032_2019_930_MOESM14_ESM.xls (36 kb)
Supplementary Table 9 (XLS 35 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Zhilan Wang
    • 1
  • Jun Wang
    • 1
    Email author
  • Jianxiang Peng
    • 2
    • 3
  • Xiaofen Du
    • 1
  • Maoshuang Jiang
    • 4
  • Yunfei Li
    • 2
    • 3
  • Fang Han
    • 5
  • Guohua Du
    • 2
    • 3
  • Huiqing Yang
    • 1
  • Shichao Lian
    • 1
  • Jianpeng Yong
    • 2
    • 3
  • Wei Cai
    • 2
    • 3
  • Juduo Cui
    • 2
    • 3
  • Kangni Han
    • 1
    • 6
  • Feng Yuan
    • 1
  • Feng Chang
    • 2
    • 3
  • Guobao Yuan
    • 2
    • 3
  • Wenna Zhang
    • 2
    • 3
  • Linyi Zhang
    • 1
  • Shuzhong Peng
    • 1
  • Hongfeng Zou
    • 2
    • 3
    Email author
  • Erhu Guo
    • 1
    Email author
  1. 1.Millet Research InstituteShanxi Academy of Agricultural Sciences/Shanxi Key Laboratory of Genetic Resources and Breeding in Minor CropsChangzhiChina
  2. 2.BGI Millet Co., LtdShenzhenChina
  3. 3.BGI Agricultural and Circular Economic Tech Co., LtdShenzhenChina
  4. 4.College of AgricultureShanxi Agricultural UniversityTaiguChina
  5. 5.Research Institute of Agriculture Sciences of Yan’anYan’anChina
  6. 6.College of BioengineeringShanxi UniversityTaiyuanChina

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