http://www.fao.org/agriculture/crops/thematic-sitemap/theme/spi/en/ Presentation by Paul Rogé, Daniel Kane and Sieg Snapp (Michigan State University) reviewing existing literature on perennial crops. The presentation was delivered in occasion of the “Putting Perennial crops to work in practice” workshop in Bamako, Mali (1-5 September 2015).

1. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
A Quantitative Review of the
Literature on Perennial Grains
Paul Rogé, Daniel Kane,
and Sieg Snapp
Michigan State University
Paul Rogé <proge@msu.edu>
4 September 2015
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 1 / 13

2. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Outline
1 The case for perennial grains
2 Perennial grains database
3 Bibliographic analysis: publications
4 Topic modeling
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 1 / 13

3. Smaje, 2015
The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
The perennial vision
• Wild floras dominated by
mixtures of perennial
plants for a renewable,
perennial-based
agriculture.
• The historical focus on
annual cultivars is
something of a puzzle.
• No insurmountable
biological obstacles exist
to develop sustainable
perennial grain crops.
• Perennial agriculture to
transform food systems.
Pigeon pea in Malawi (2014)
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 2 / 13

4. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
historical precedent & justification
• Breeding efforts
undertaken in different
parts of the world since
the 1930s.
• Prior perennial grains
research is broad and
diffuse, which challenges a
coherent synthesis of
research.
• A review using
quantitative methods may
help us better understand
the progression of
perennial grains research.
Perennial sorghum at
the Land Institute (2014)
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 3 / 13

5. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Queries for the perennial grains literature
Databases Web of Science, Scopus, ScienceDirect, and AGRICOLA
Crops rice, wheat, rye, sorghum, and pigeonpea
Inclusion
Terms #1
Inclusion Terms #2 Word
Proximity
Exclusion
Term
perennial wheat, grain, triticum, secale,
pigeonpea, cajanus, rice, oryza
1
perennial rye 1 ryegrass
long
duration
pigeon pea , cajanus 1
ratoon sorghum, pigeon pea, cajanus,
rice, oryza
5
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 4 / 13

6. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Assembling the perennial grains database
• Refined from 3026
to 950 records
• WoS, Scopus, and
ScienceDirect
retrieved the most
unique records
• AGRICOLA retrieved
the fewest unique
records
82
79
695
1
24
9
20
1
6
6
1 0
22
29
0
AGRICOLA
(47)
ScienceDirect
(82)
Scopus
(237)
Web of Science
(835)
(a) DATABASES
pigeonpea
(47)
(b) CROPS
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 5 / 13

7. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Assembling the perennial grains database
• Queries for rice
yielded the most
results
• Queries for wheat
and rye overlapped
• Queries for rice
overlapped
somewhat with
those for wheat and
sorghum
6
1 0
22
0
41
485
95
88
14231
04
2
4
2
0 0
6
1
4
000
0
0
0
0
0
21
0
0
0
0
0
pigeonpea
(47)
rice
(502)
rye
(133)
sorghum
(106)
wheat
(185)
(b) CROPS
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 5 / 13

8. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Observations on the perennial grains database
• Overlap in research due to agronomic compatibility
between crops and their genetic relatedness.
• Crops like rice and sorghum may be grown in the the
mosaic of diversified farming systems.
• Hybridization common between wheat and rye.
• Rice research had a greater number of publications
compared to other grains, due to the existance of a
perennial species of rice, and ratooning rice to obtain 2-3
consecutive crops is a traditional agricultural practice in
some regions of the world.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 6 / 13

9. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Observations on the perennial grains database
• Overlap in research due to agronomic compatibility
between crops and their genetic relatedness.
• Crops like rice and sorghum may be grown in the the
mosaic of diversified farming systems.
• Hybridization common between wheat and rye.
• Rice research had a greater number of publications
compared to other grains, due to the existance of a
perennial species of rice, and ratooning rice to obtain 2-3
consecutive crops is a traditional agricultural practice in
some regions of the world.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 6 / 13

10. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Observations on the perennial grains database
• Overlap in research due to agronomic compatibility
between crops and their genetic relatedness.
• Crops like rice and sorghum may be grown in the the
mosaic of diversified farming systems.
• Hybridization common between wheat and rye.
• Rice research had a greater number of publications
compared to other grains, due to the existance of a
perennial species of rice, and ratooning rice to obtain 2-3
consecutive crops is a traditional agricultural practice in
some regions of the world.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 6 / 13

11. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Publications across time
Research began in
the 1930s, and
has steadily
increased. The
journal articles
published in the
last five years has
approached the
same count as the
prior decade. The
term perennial
grain gained
prominence since
2000.
0
100
200
1920−19301930−19401940−19501950−19601960−19701970−19801980−19901990−20002000−20102010−2015
Perennial Grains
Pigeonpea
Rice
Rye
Sorghum
Wheat
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 7 / 13

12. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Publications across time
The Soviet Unioin
published
extensively on rye
and wheat from
the 1930s to
1960s, in such
publications as
Selektsiya i
Semenvodstvo
(Breeding and
Seed Production).
The period from
1961 to 1990
highlighted IRRI
publications.
1930−1960 1961−1990 1991−2015
ACTA AGRONOMICA SINICA
AGRICULTURE ECOSYSTEMS AND ENVIRONMENT
AGRONOMY JOURNAL
BJULLETEN GLAVNOGO BOTANICHESKOGO SADA
BULL APPL BOT LENINGRAD SER A
DOKLADY AKADEMII NAUK SSSR
FIELD CROPS RESEARCH
HYBRID RICE
INTERNATIONAL RICE RESEARCH NEWSLETTER
MADRAS AGRICULTURAL JOURNAL
ORYZA
PHILIPPINE JOURNAL OF CROP SCIENCE
SELEKTSIYA I SEMENOVODSTVO
SOVIET NEWS
0 10 20 30 0 10 20 30 0 10 20 30
Count
Publication
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 7 / 13

13. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Publications across time
High impact
publications
began to feature
perennial grains
research since the
1990s. Rice
increased
dramatically in the
1980s. Sorghum
and pigeonpea
remain of interest
in regions of
historical
importance.
1930−1960 1961−1990 1991−2015
ACTA AGRONOMICA SINICA
AGRICULTURE ECOSYSTEMS AND ENVIRONMENT
AGRONOMY JOURNAL
BJULLETEN GLAVNOGO BOTANICHESKOGO SADA
BULL APPL BOT LENINGRAD SER A
DOKLADY AKADEMII NAUK SSSR
FIELD CROPS RESEARCH
HYBRID RICE
INTERNATIONAL RICE RESEARCH NEWSLETTER
MADRAS AGRICULTURAL JOURNAL
ORYZA
PHILIPPINE JOURNAL OF CROP SCIENCE
SELEKTSIYA I SEMENOVODSTVO
SOVIET NEWS
0 10 20 30 0 10 20 30 0 10 20 30
Count
Publication
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 7 / 13

14. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Observations on publication counts
• While research on perennial crops is increasing overall,
there appear to have been distinct periods of active
research for each crop.
• The transition from exploratory phases with dialog
between specific communities of researchers to
eventually gain prominence in more general publications.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 8 / 13

15. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Observations on publication counts
• While research on perennial crops is increasing overall,
there appear to have been distinct periods of active
research for each crop.
• The transition from exploratory phases with dialog
between specific communities of researchers to
eventually gain prominence in more general publications.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 8 / 13

16. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Observations on publication counts
• IRRI led the research on perennial grains during the 1980s
and 1990s, while journal articles on perennial wheat and
rye were primarily featured in publications from the Soviet
Union in the early 20th century.
• The comparative success of rice suggests that
perennializing crops requires long-term efforts, which may
be more easily achieved in institutional settings.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 8 / 13

17. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Observations on publication counts
• IRRI led the research on perennial grains during the 1980s
and 1990s, while journal articles on perennial wheat and
rye were primarily featured in publications from the Soviet
Union in the early 20th century.
• The comparative success of rice suggests that
perennializing crops requires long-term efforts, which may
be more easily achieved in institutional settings.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 8 / 13

18. Grün and Hornik, 2011
The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
“Reading” abstracts with topic modeling
• Topics are modeled by analyzing how frequently groups of
words co-occur in a given body of literature.
• We chose to model three topics a priori, and used the
Gibbs LDA to generate posterior probability estimates for
topic terms and for the assignment of journal articles.
• We conducted this analysis in three ways:
1 the global library between 1930 and 2015
2 individual crop libraries between 1930 and 2015
3 the global library for journal articles published between
1930-1959, 1960-1989, and 1990-2015
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 9 / 13

19. Grün and Hornik, 2011
The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
“Reading” abstracts with topic modeling
• Topics are modeled by analyzing how frequently groups of
words co-occur in a given body of literature.
• We chose to model three topics a priori, and used the
Gibbs LDA to generate posterior probability estimates for
topic terms and for the assignment of journal articles.
• We conducted this analysis in three ways:
1 the global library between 1930 and 2015
2 individual crop libraries between 1930 and 2015
3 the global library for journal articles published between
1930-1959, 1960-1989, and 1990-2015
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 9 / 13

20. Grün and Hornik, 2011
The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
“Reading” abstracts with topic modeling
• Topics are modeled by analyzing how frequently groups of
words co-occur in a given body of literature.
• We chose to model three topics a priori, and used the
Gibbs LDA to generate posterior probability estimates for
topic terms and for the assignment of journal articles.
• We conducted this analysis in three ways:
1 the global library between 1930 and 2015
2 individual crop libraries between 1930 and 2015
3 the global library for journal articles published between
1930-1959, 1960-1989, and 1990-2015
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 9 / 13

21. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Topics by decade for the global library
Crop Science
Topic 1 moderately
increases in the
1990s. The
associated terms
suggest agronomic
studies that are
concerned with crop
productivity and soil
health at the field
scale.
0
25
50
75
100
1930
1940
1950
1960
1970
1980
1990
2000
2010
Decade
Count
Selected
Topic Terms
TOPIC 1
plant
product
soil
seed
field
TOPIC 2
ratoon
crop
yield
main
ratoon crop
TOPIC 3
perenni
annual
hybrid
resist
wild
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 10 / 13

22. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Topics by decade for the global library
Agroecology (rice)
Topic 2 increases
dramatically from the
1980s to the present.
The associated terms
also suggest research
in agronomy,
however with a focus
on management
practices like
ratooning.
0
25
50
75
100
1930
1940
1950
1960
1970
1980
1990
2000
2010
Decade
Count
Selected
Topic Terms
TOPIC 1
plant
product
soil
seed
field
TOPIC 2
ratoon
crop
yield
main
ratoon crop
TOPIC 3
perenni
annual
hybrid
resist
wild
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 10 / 13

23. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Topics by decade for the global library
Breeding (wheat)
Topic 3 declines from
1930 and 1970, and
then increases from
1980 to the present.
The associated terms
suggest breeding
studies that may
involve the
hybridization of
annual and perennial
species for greater
crop resistance.
0
25
50
75
100
1930
1940
1950
1960
1970
1980
1990
2000
2010
Decade
Count
Selected
Topic Terms
TOPIC 1
plant
product
soil
seed
field
TOPIC 2
ratoon
crop
yield
main
ratoon crop
TOPIC 3
perenni
annual
hybrid
resist
wild
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 10 / 13

24. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Journal articles assigned to the topics
Topic 1: Crop Science
Article Prob
Scherr, S.J., Sthapit, S. (2009) Mitigating climate change through
food and land use. Worldwatch Paper
0.7663
Cheng, C. H., Huang, S. H. (2004) Population fluctuations and
forecasting of the white-backed planthopper, Sogatella furcifera
on rice in Chiayi region, Taiwan. Plant Protection Bulletin
(Taichung)
0.6787
Piper, J.k. (1993) Soil water and nutrient change in stands of
three perennial crops. Soil Science Society of America
0.6771
Hulugalle, N.R., Lal, R. (1986) Root growth of maize in a com-
pacted gravelly tropical alfisol as affected by rotation with a
woody perennial. Field Crops Research
0.6299
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 11 / 13

25. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Journal articles assigned to the topics
Topic 2: Agroecology (rice)
Article Prob
Nakano, Hiroshi, Morita, Satoshi (2008) Effects of time of first
harvest, total amount of nitrogen, and nitrogen application
method on total dry matter yield in twice harvesting of rice. Field
Crops Research
0.8194
Zhen-xie, Yi, Nai-mei, Tu, Ping-ping, Chen (2005) Source-sink
characteristics of main crop and ratooning rice of several new
hybrid rice combinations. Zhongguo Shuidao Kexue
0.7789
ZhenXie, Yi, NaiMei, Tu, PingPing, Chen (2005) Source-sink char-
acteristics of main crop and ratoon crop of several new hybrid
rice combinations. Chinese Journal of Rice Science
0.7537
FuXian, Xu, Hong, Xiong, Lin, Zhang, XiaoYi, Guo, YongChuan,
Zhu, XingBing, Zhou, Mao, Liu (2009) Effects of the decreased
index of SPAD value of leaf after full heading on ratooning ability.
Scientia Agricultura Sinica
0.7467
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 11 / 13

26. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Journal articles assigned to the topics
Topic 3: Breeding (wheat)
Article Prob
FIRSOVA, M. K. (1948) Research Institutes in struggles for har-
vests.. Selektsiya i semenovodstvo
0.7246
PRUTSKOVA, M. G. (1934) Breeding grain crops.. Bull. Appl. Bot.
Leningrad, Ser. A
0.6894
ALDANOV, A. D. (1936) 25 years work of Saratov Central Station
of plant-breeding and genetics.. Sotsialisticheskoe Zernovoe
Khozyaistvo
0.675
GORSKOV, I., JAKOVLEV, P. (1934) The possibilities revealed by
the achievements of I. V. Michurin.. Sotsialisticeskaja Rekon-
struktsija Sel’skogo Khozjaistva (Socialist Reconstruction of Agri-
culture)
0.6749
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 11 / 13

27. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Observations on modeling the global library
• Modeling the global library reflects the literature on the
most prominent literature, notably rice and wheat.
• An essential step to correctly interpreting the topic terms
was to review the assigned journal articles.
• An initial analysis of the global library suggests that the
perennial grains literature extends beyond the limits of
plant breeding, covering a host of issues associated with
agriculture and the environment.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 12 / 13

28. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Summary
• Perennial grains research in has thrived for crops which
had a historically been managed as perennials, as in the
case of rice. This legacy provides a strong foundation for
research and innovation.
• Crops like sorghum and pigeon pea also may be ratooned.
There is a need for more research to develop and manage
these grain crops as perennials in sub-Saharan Africa.
• Continuity in institutional support would greatly advance
the introduction of perennial grain crops into farming
systems given clearly demarcated historical moments of
research.
• Topic modeling is promising for the interpretation of
disparate body of literature.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 13 / 13

29. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Summary
• Perennial grains research in has thrived for crops which
had a historically been managed as perennials, as in the
case of rice. This legacy provides a strong foundation for
research and innovation.
• Crops like sorghum and pigeon pea also may be ratooned.
There is a need for more research to develop and manage
these grain crops as perennials in sub-Saharan Africa.
• Continuity in institutional support would greatly advance
the introduction of perennial grain crops into farming
systems given clearly demarcated historical moments of
research.
• Topic modeling is promising for the interpretation of
disparate body of literature.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 13 / 13

30. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Summary
• Perennial grains research in has thrived for crops which
had a historically been managed as perennials, as in the
case of rice. This legacy provides a strong foundation for
research and innovation.
• Crops like sorghum and pigeon pea also may be ratooned.
There is a need for more research to develop and manage
these grain crops as perennials in sub-Saharan Africa.
• Continuity in institutional support would greatly advance
the introduction of perennial grain crops into farming
systems given clearly demarcated historical moments of
research.
• Topic modeling is promising for the interpretation of
disparate body of literature.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 13 / 13

31. The case for perennial grains Perennial grains database Bibliographic analysis: publications Topic modeling
Summary
• Perennial grains research in has thrived for crops which
had a historically been managed as perennials, as in the
case of rice. This legacy provides a strong foundation for
research and innovation.
• Crops like sorghum and pigeon pea also may be ratooned.
There is a need for more research to develop and manage
these grain crops as perennials in sub-Saharan Africa.
• Continuity in institutional support would greatly advance
the introduction of perennial grain crops into farming
systems given clearly demarcated historical moments of
research.
• Topic modeling is promising for the interpretation of
disparate body of literature.
Paul Rogé (proge@msu.edu) Quantitative Review 4 September 2015 13 / 13